
1001. Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [RNA-Seq]
(Submitter supplied) Anaplastic thyroid carcinoma (ATC) is one of the most aggressive malignancy and accounts for the majority of thyroid cancer-related deaths. Despite intensive research, there remains no effective treatment for patients with ATC. Here, we identify THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), as a potent anti-ATC compound by high-throughput chemical screening. ATC cells, but not papillary thyroid cancer (PTC) cells, are exceptionally sensitive to CDK7 inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120176/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491864
Series		Accession: GSE120176	ID: 200120176

1002. Separation of breast cancer and organ microenvironment transcriptomes in metastases
(Submitter supplied) The seed-and-soil hypothesis was described over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated, however, the genetic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. In these studies, a set of human breast cancer patient-derived xenograft (PDX) metastasis models were utilized. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL22245 128 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118942/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487493
Series		Accession: GSE118942	ID: 200118942

1003. Specific inhibition of DPY30 activity by peptides suppresses blood cancer cell growth
(Submitter supplied) Epigenetic modulators are being recognized as attractive targets for potential cancer treatment. SET1/MLL complexes are the major H3K4 methyltransferase complexes in mammals. The DPY30 subunit is associated with these complexes by forming a dimer that directly binds to the ASH2L subunit in the complexes and facilitates methylation. We have previously established an important role of DPY30 in certain hematologic malignancies including MLL-rearranged leukemia and Burkitt’s lymphoma, but the domain on DPY30 that regulates cancer growth is not evident. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476705
Series		Accession: GSE115988	ID: 200115988

1004. Illumina HiSeq Sequencing on Breast cancer PDX samples
(Submitter supplied) RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 50 Cycle Single-Read Sequencing v4
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 19 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113986/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454798
Series		Accession: GSE113986	ID: 200113986

1005. Preclinical model of obesity and ER-positive breast cancer
(Submitter supplied) Here, we developed a mouse model of diet induced obesity that is graft competent.  In this model, we grew an ER-positive breast cancer patient derived tumor.  Following ovariectomy and estrogen deprivation therapy, tumors continued to grow in obese but not lean mice.  RNAsequencing analysis was performed on tumors from estrogen-supplemented lean mice, and from lean and obese mice after estrogen deprivation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434156
Series		Accession: GSE110644	ID: 200110644

1006. LINC00261 is an epigenetically-regulated tumor suppressor that is essential for activation of the DNA damage response [H522-LINC00261 RNA-seq data set]
(Submitter supplied) Lung cancer is the leading cause of cancer-related death in the United States. Long non-coding RNAs (lncRNAs) are a class of regulatory molecules whose role in lung carcinogenesis is poorly understood. In this study, we profiled lncRNA expression in lung adenocarcinoma (LUAD) cell lines, compared their expression to that of purified alveolar epithelial type II cells (the purported cell of origin for LUAD), cross-referenced these with lncRNAs altered in primary human tumors, and interrogated for lncRNA whose expression correlated with patient survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110182/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433043
Series		Accession: GSE110182	ID: 200110182

1007. LINC00261 is an epigenetically-regulated tumor suppressor that is essential for activation of the DNA damage response
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110025/
Series		Accession: GSE110025	ID: 200110025

1008. Defining transcription factor networks that govers SCC growth
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 GPL21103 36 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104145/
Series		Accession: GSE104145	ID: 200104145

1009. A Suv39H1-low chromatin state drives migratory cell populations in cervical cancer 
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL15433 14 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103794/
Series		Accession: GSE103794	ID: 200103794

1010. A Suv39H1-low chromatin state drives migratory cell populations in cervical cancer [RNA-Seq]
(Submitter supplied) The evolution of migratory populations of cells within solid tumours represents a critical stage during cancer metastasis. We have previously reported the enhanced migratory properties of one such population, marked by the expression of CD66, within cervical cancers. However, it is not clear what mechanisms drive such migratory populations, and how these cells would retain a “memory” of initial migration-inducing cues during metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103792/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407073
Series		Accession: GSE103792	ID: 200103792

1011. Macrophage polarization controlled by fibroblast crosstalk and targeted by medications in rheumatoid arthritis
(Submitter supplied) In this study, we performed RNAseq on human macropahges following a tumor necrosis factor response with and without human fibroblasts, the representative stromal cell type in the synovial lining of joints that become activated during inflammatory arthritis. Our RNAseq analysis reveals a crosstalk pathway between macrophages and fibroblasts that emerges as a result of co-culture that we call the MTF polarization phenotype. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 74 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95588/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377567
Series		Accession: GSE95588	ID: 200095588

1012. A novel Menin-MLL inhibitor induces specific chromatin changes and eradicates disease in models of MLL-rearranged leukemia
(Submitter supplied) Inhibition of the Menin (encoded by MEN1) and MLL1 (KMT2A) protein-protein interaction has been proposed as a potential targeted therapeutic strategy for MLL-rearranged (MLL-r) leukemia. We sought to develop more potent and selective Menin-MLL1 interaction inhibitors that are effective in vitro and in vivo to directly assess potential therapeutic opportunities. Structure-based design yielded the potent, highly selective and orally-bioavailable small molecule inhibitor VTP-50469. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 224 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127298/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524685
Series		Accession: GSE127298	ID: 200127298

1013. Differently expressed gene analysis in HeLa cells expressing high levels of phosphorylated PCNA
(Submitter supplied) Cells expressing phosphorylation-mimicking PCNA, PCNA-Y211D, show elevated hallmarks specific to the epithelial-mesenchymal transition (EMT), including the upregulation of EMT-promoting factor Snail and the downregulation of EMT-inhibitory factors E-cadherin and GSK3β. These cells exhibit active cell migration and also undergo G2/M arrest. Interestingly, all of these EMT-associated activities require the activation of ATM and Akt, as inactivating these protein kinases by gene knockdown or inhibitors blocks EMT-associated signaling and cell migration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE127nnn/GSE127276/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524654
Series		Accession: GSE127276	ID: 200127276

1014. Targeting Transcriptional Addiction by a Novel Highly Selective CDK9 Kinase Inhibitor for AML.
(Submitter supplied) we reported a novel CDK9 high selective inhibitor JSH-009, it displayed high potency against CDK9 (IC50=1nM) and achieved high selectivity over CDKs family kinases (range from 200-10000 fold). JSH-009 showed high potent anti-proliferation effect in a range of AML cells and primary patient cells through downregulation of a number of transcriptional, apoptotic genes and related signaling pathways. In addition, this compound exhibited great anti-leukemic efficacy in the MV4-11 mediated xenograft, engraftment and AML PDX preclinical models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123287/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508101
Series		Accession: GSE123287	ID: 200123287

1015. Spontaneously slow-cycling subpopulations of human cells originate from activation of stress response pathways
(Submitter supplied) Slow-cycling subpopulations exist in bacteria, yeast, and mammalian systems. In the case of cancer, slow-cycling subpopulations have been proposed to give rise to drug resistance. However, the origin of slow-cycling human cells is poorly studied, in large part due to lack of markers to identify these rare cells. Slow-cycling cells pass through a non-cycling period marked by low CDK2 activity and high p21 levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122927/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506946
Series		Accession: GSE122927	ID: 200122927

1016. Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CRC_ATAC]
(Submitter supplied) Lineage tracing provides unprecedented insights into the fate of individual cells and their progeny in complex organisms. While effective genetic approaches have been developed in vitro and in animal models, these cannot be used to interrogate human physiology in vivo. Instead, naturally occurring somatic mutations have been utilized to infer clonality and lineal relationships between cells in human tissues, but current approaches are limited by high error rates and scale, and provide little information about the state or function of the cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122583/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505668
Series		Accession: GSE122583	ID: 200122583

1017. Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CRC_scRNA]
(Submitter supplied) Lineage tracing provides unprecedented insights into the fate of individual cells and their progeny in complex organisms. While effective genetic approaches have been developed in vitro and in animal models, these cannot be used to interrogate human physiology in vivo. Instead, naturally occurring somatic mutations have been utilized to infer clonality and lineal relationships between cells in human tissues, but current approaches are limited by high error rates and scale, and provide little information about the state or function of the cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 272 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122582/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505670
Series		Accession: GSE122582	ID: 200122582

1018. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity
(Submitter supplied) Acute myeloid leukemia (AML) is a heterogeneous disease that resides within a complex microenvironment, complicating efforts to understand how different cell types contribute to disease progression. We combined single-cell RNA sequencing and genotyping to profile 38,410 cells from 40 bone marrow aspirates, including 16 AML patients and five healthy donors. We then applied a machine learning classifier to distinguish a spectrum of malignant cell types whose abundances varied between patients and between subclones in the same tumor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL24106 83 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116256/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477870
Series		Accession: GSE116256	ID: 200116256

1019. Human lineage tracing enabled by mitochondrial mutations and single cell genomics
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL15520 2733 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115218/
Series		Accession: GSE115218	ID: 200115218

1020. GREB1 amplifies androgen receptor output in prostate cancer and contributes to antiandrogen resistance
(Submitter supplied) Genomic amplification of the androgen receptor (AR) is an established mechanism of antiandrogen resistance in prostate cancer.  Here we show that the magnitude of AR signaling output, independent of AR genomic alteration or expression level, also contributes to antiandrogen resistance, through upregulation of the coactivator GREB1.  We demonstrate 100-fold heterogeneity in AR output within cell lines and show that cells with high AR output have reduced sensitivity to enzalutamide. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120720/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494242
Series		Accession: GSE120720	ID: 200120720

1021. New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; synthetic construct
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL25329 60 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117366/
Series		Accession: GSE117366	ID: 200117366

1022. New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [miRNA-Seq]
(Submitter supplied) Microarray analysis of the miRNome in multiple myeloma (MM) has unraveled the differential expression of miRNAs in cytogenetic subgroups, their involvement in the tumor biology and their effectiveness in prognostic models. Herein, we provide a view of small RNA transcriptional landscape in MM at a higher definition, exploiting the possibilities offered by small RNA-sequencing (sRNA-seq), including improved detection of known/new mature species and accurate investigation of isomiRs and miRNA-offset RNAs (moRNAs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481916
Series		Accession: GSE117365	ID: 200117365

1023. Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL18573 87 Samples
FTP download: GEO (BED, BW, HIC, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116876/
Series		Accession: GSE116876	ID: 200116876

1024. Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [DND41_RNA-seq]
(Submitter supplied) Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480475
Series		Accession: GSE116873	ID: 200116873

1025. Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [HCC1599_RNA-seq]
(Submitter supplied) Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116870/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480470
Series		Accession: GSE116870	ID: 200116870

1026. Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_RNA-seq]
(Submitter supplied) Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116867/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480469
Series		Accession: GSE116867	ID: 200116867

1027. RNA-seq analysis and shRNA screen of breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113653/
Series		Accession: GSE113653	ID: 200113653

1028. RNA-seq analysis of breast cancer
(Submitter supplied) Background: We searched triple negative breast cancer (TNBC) specifically expressing candidates for target therapy.  Methods: High expressing genes in three TNBC cell lines compared to three non-TNBC cell lines were evaluated by using RNA sequencing (log2 ratio>5, q<0.05). By integrating the shRNA library screening and public gene expression databases, we identifyied candidates for therapeutic targets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113650/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453538
Series		Accession: GSE113650	ID: 200113650

1029. circRNA profile in hypopharyngeal cancer
(Submitter supplied) 3 normal samples and 3 tumor samples were sequenced
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111423/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436974
Series		Accession: GSE111423	ID: 200111423

1030. IKZF1 as a Master Regulator of Immune Infiltrate Recruitment in Solid Tumors
(Submitter supplied) Regulatory network analysis of TCGA tumor cohorts to identify MR-based susceptibility to immune infiltration enhancement therapy
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 27 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436150
Series		Accession: GSE111201	ID: 200111201

1031. ONECUT2 Drives Neuroendocrine Prostate Cancer Through Hypoxia Signaling
(Submitter supplied) To determine the underlying mechanism of ONECUT2 in prostate cancer hypoxia, we conducted a series of RNA-Seq and ChIP-Seq experiments in LNCaP and PC3 cells under normoxia and hypoxia conditions. We did RNA-Seq in LNCaP cells with or without OC2 overexpression and in PC3 cells with or without OC2 knockdown. We used anti-Flag antibody to perform the ChIP-Seq experiment in PC3 cells with Flag and OC2 fusion protein overexpression. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 28 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416257
Series		Accession: GSE106305	ID: 200106305

1032. PTENα/β paradoxically promote carcinogenesis through WDR5-H3K4me3 axis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL24676 13 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126984/
Series		Accession: GSE126984	ID: 200126984

1033. PTENα/β paradoxically promote carcinogenesis through WDR5-H3K4me3 axis [RNA-seq]
(Submitter supplied) we report that USP9X and FBXW11 selectively regulate the stability of PTENα/β but not PTEN proteins by deubiqitination and ubiquitination respectively. USP9X promotes and FBXW11 suppresses tumorigenesis mediated by PTENα/β. In contrast to the current paradigm for PTEN as a tumor suppressor, PTENα/β promote tumorigenesis of cancer cells in a phosphatase-independent manner. Mechanistically, PTENα/β localized in the nucleus regulate expressions of tumor-promoting genes such as NOTCH3 in the similar way as the H3K4 presenter WDR5. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126983/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA524002
Series		Accession: GSE126983	ID: 200126983

1034. Transcriptomic profiling of head and neck squamous cell carcinoma cell lines
(Submitter supplied) Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer world wide, and survival rates range from 40-80% depending on subsite.  As novel treatment strategies are investigated, comprehensively characterized cell lines representative of the diversity seen in patients will be crucial to correlating genetic and phenotypic features with therapeutic response.  The University of Michigan has generated a large panel of HNSCC cell lines that are utilized in laboratories worldwide. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 41 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126975/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523940
Series		Accession: GSE126975	ID: 200126975

1035. Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL6244 GPL16686 GPL18573 74 Samples
FTP download: GEO (CEL, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124438/
Series		Accession: GSE124438	ID: 200124438

1036. Transcriptomic Profiling of Circulating Tumor Cells in Multiple Myeloma: A New Model to Understand Disease Dissemination III
(Submitter supplied) The number of peripheral blood (PB) circulating tumor cells (CTCs) predicts risk of transformation in smoldering multiple myeloma (MM) and survival in active MM. Growing evidence suggests that as the tumor progresses and the microenvironment becomes hypoxic, clonal plasma cells (PCs) constantly invade new regions of the bone marrow (BM) through induced systemic recirculation. Of note, the frequency of CTCs is typically low and thus, it could be hypothesized that the dissemination of MM is made by few tumor cells with unique features that induce them to egress the BM and spread the disease through PB. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512009
Series		Accession: GSE124437	ID: 200124437

1037. Single cell RNA-seq of 25 thousand epithelial cells from xenografts of triple-negative breast cancers
(Submitter supplied) Patient derived xenografts (PDX) were created from two triple-negative breast cancers (PDX-110 and PDX-332) taken at the time of surgery from drug-naive patients. Freshly sorted epithelial cells were profiled by single-cell RNA-seq (scRNA-seq) using a 10X Genomics Chromium System.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510333
Series		Accession: GSE123926	ID: 200123926

1038. Gene expression profile in FTSEC cells (FT190 and FT194 cell lines) transduced with shRNA to knockdown RNF20 or with control shRNA using RNA-seq.
(Submitter supplied) We identified that downregulation of RNF20/H2Bub1 is involved in HGSOC progression through altering key immune signaling pathways. The goal of this RNA-seq is to analyze gene expression profile in FTSEC cells (FT190 and FT194 cell lines) with RNF20 knockdown (shRNF20) or control shRNA. Integrating the data from ATAC-seq for same samples, we observed that expression of immune signaling pathways have significantly changed by RNF20/H2Bub1 downregulation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504052
Series		Accession: GSE122237	ID: 200122237

1039. RNA seq comparison between scrambled and shGRP78 cells
(Submitter supplied) Pancreatic cancer cells transduced with sh knockdown of GRP78
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115849/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476305
Series		Accession: GSE115849	ID: 200115849

1040. Genome-wide transcriptional response to random aneuploidy in human cells
(Submitter supplied) Previous studies on transcriptional response to aneuploidy have focused on comparing model cell lines harbouring defined aneuploidy (specific chromosomes) with their parental diploid cell lines. However, the majority of tumours are composed of cancer cells with complex karyotypes (diverse chromosome assortment). Despite this fact, proven functions of random aneuploidies in promoting tumourigenesis are lacking. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431296
Series		Accession: GSE109519	ID: 200109519

1041. Transcriptome analysis of TP53-R248L overexpressed 19NS patient-derived glioblastoma cells
(Submitter supplied) This study demonstrates the role of TP53 gain-of-function (GOF) mutation on glioblastoma progression. However, little is known about the transcriptional alteration upon TP53 GOF mutation. In this study, we found that TP53 GOF mutation (R248L mutation) promotes the enrichment of multiple gene signatures related to inflammation and chemotaxis. Particularly, through in vitro and in vivo approaches, we verified that TP53 GOF mutation enhances NFKB signaling which in turn up-regulates CCL2 and TNFA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23525 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396062
Series		Accession: GSE101980	ID: 200101980

1042. COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [DF]
(Submitter supplied) Tumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single cell RNA-sequencing in an orthotopic mouse prostate cancer model, we find upregulation of Prolactin receptor as cancer cells that have disseminated to the lung expand into micrometastases. Secretion of the ligand Prolactin by adjacent lung stromal cells is induced by tumor cell production of the COX-2 synthetic product prostaglandin E-2 (PGE-2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126158/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521167
Series		Accession: GSE126158	ID: 200126158

1043. Differential YAP expression in glioma cells induces cell competition and promotes tumorigenesis
(Submitter supplied) Intratumor heterogeneity associates with cancer progression and may account for a substantial portion of therapeutic resistance. Although extensive studies have focused on the origin of the heterogeneity, biological interactions between heterogeneous malignant cells within a tumor are largely unexplored. Glioblastoma (GBM) is the most aggressive primary brain tumor. Here, we found that the expression of Yes-associated protein (YAP) is intratumorally heterogeneous in GBM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123755/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509696
Series		Accession: GSE123755	ID: 200123755

1044. FTSEC cells (FT190 and FT194 cell lines) transduced with shRNA to knockdown RNF20 or with control shRNA
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL16791 24 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122238/
Series		Accession: GSE122238	ID: 200122238

1045. Inhibition of TAZ contributes radiation-induced senescence and growth arrest in glioma cells
(Submitter supplied) Glioblastoma (GBM) is the most aggressive brain tumor and resistant to current available therapeutics, such as radiation. To improve the clinical efficacy, it is important to understand the cellular mechanisms underlying tumor responses to radiation. Here, we investigated long-term cellular responses of human GBM cells to ionizing radiation. Comparing to the initial response within 12 hours, gene expression modulation at 7 days after radiation is markedly different. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121422/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497297
Series		Accession: GSE121422	ID: 200121422

1046. The induction of core pluripotency master regulators in cancers defines poor clinical outcomes and treatment resistance
(Submitter supplied) Clinical expression of core pluripotent stem cell master regulators OCT4, SOX2 and NANOG is associated with treatment resistance and lethal cancers. We have described a novel model to induce the expression of these factors in vitro. We term this culture environment ‘Acquired Pluripotent Stem Cell Environment (APSCE)’ and RNA-seq comparisons were made to culture in conventional serum supplemented ‘Full Media’ (FM) in human prostate (LNCaP, CWR22Rv1) and bladder (RT112) cancer cell lines. Depletion of the androgen receptor (AR) with siRNA targeting exon1(siEX1) was additionally performed in the CWR22Rv1 cell line alongside a scrambled control (siCTRL). 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117193/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481377
Series		Accession: GSE117193	ID: 200117193

1047. Fisetin induces autophagy in pancreatic cancer cells via endoplasmic reticulum stress- and mitochondrial stress-dependent pathways
(Submitter supplied) Pancreatic cancer is one of the most aggressive tumors and has poor survival rates. Fisetin, a natural flavonoid, was recently reported to have antitumor effects in various cancer models. Autophagy is a conserved catabolic process that maintains cellular homoeostasis in response to stress, and together with apoptosis, determines cell fate. Herein, we examined the effect of fisetin on pancreatic cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481372
Series		Accession: GSE117189	ID: 200117189

1048. Targeting an RNA-binding Protein Splicing Network in Acute Myeloid Leukemia
(Submitter supplied) RNA-binding proteins (RBPs) are essential modulators of transcription and translation and are often dysregulated in cancer. Here we systematically interrogated RBP vulnerabilities in acute myeloid leukemia (AML) by performing a comprehensive CRISPR/Cas9 screen, targeting the RNA-binding domains of all classical RBPs. Our screen revealed RBPs that are exclusively required for leukemia survival, including the splicing factor RBM39. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 39 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114558/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471804
Series		Accession: GSE114558	ID: 200114558

1049. COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 164 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96676/
Series		Accession: GSE96676	ID: 200096676

1050. Combinatorial inhibition of Notch and FLT3 exerts synergistic cytotoxic effects in FLT3/ITD+ acute myeloid leukemia
(Submitter supplied) we observed synergistic cytotoxic effects, preferentially reducing cell proliferation and inducing apoptosis in FLT3/ITD+ AML cell lines and in primary AML cells. Furthermore, the combination of FLT3-TKI and GSI eradicated leukemic cells and prolonged survival in a FLT3/ITD+ patient derived xenograft (PDX) AML model. Mechanistically, decreased expression of CXCR3 that lead to down-regulated ERK signaling was partially responsible for the observed synergy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126933/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523802
Series		Accession: GSE126933	ID: 200126933

1051. The splicing factor U2AF1 contributes to cancer progression through a non-canonical role in translation regulation
(Submitter supplied) Somatic mutations in the spliceosome have emerged in recent years as oncogenes in human cancer. These mutations are in the factors involved in splice site selection, including a missense mutation (Ser34Phe) in a conserved nucleic acid binding domain of the spicing factor U2AF1. This protein plays a critical role in recognition of the 3'-splice site and assembly of the pre-spliceosomal complex. However, the role that this mutation plays in oncogenesis is still unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL21290 39 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126912/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523666
Series		Accession: GSE126912	ID: 200126912

1052. Integrative analysis of mRNA and lncRNA profiles identified pathogenetic  lncRNAs  in esophageal squamous cell carcinoma
(Submitter supplied) Systems biology approaches can help understand pathogenesis of complex human diseases like cancers for identification of potential new therapeutic targets. Here in this study, we performed genome-wide screening for mRNA and lncRNA profiles in esophageal cancer to identify the novel cancer-related mRNA and lncRNA in esophageal squamous cell carcinoma (ESCC). We identified 3000 up-regulated/2517 down-regulated mRNAs and 402 up-regulated/741 down-regulated lncRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111011/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435587
Series		Accession: GSE111011	ID: 200111011

1053. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines Cel-seq]
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126908/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523631
Series		Accession: GSE126908	ID: 200126908

1054. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines 10X]
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126906/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523629
Series		Accession: GSE126906	ID: 200126906

1055. Neural cell adhesion molecule 1 (NCAM1; CD56) promotes leukemogenesis and confers drug resistance in acute myeloid leukemia.
(Submitter supplied) Neural cell adhesion molecule 1 (NCAM1; also known as CD56) is expressed in up to 20% of acute myeloid leukemia (AML) patients. Expression of NCAM1 is widely used as a marker of minimal residual disease; however, the biological function of this cell surface protein in AML remains elusive. In this study we investigated the impact of aberrant NCAM1 expression on leukemogenesis, drug resistance and its role as a biomarker to guide therapy.Gene expression profiling was performed with RNA-seq in three cell lines (SKM-1, NOMO-1, MOLM-14) after doxycycline-mediated induction of scrambled shRNA or shNCAM1 at timepoint 72 hours.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507440
Series		Accession: GSE123071	ID: 200123071

1056. HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells
(Submitter supplied) HOXC6 is a member of the HOX family, and its aberrant expression has been verified in a variety of cancers, such as prostate, breast,nasopharyngeal carcinoma,gastric, and ovarian cancers.Some studies suggest that HOXC6 might be involved in tumor initiation and progression.However, the role of HOXC6 in esophageal squamous cell carcinoma cells has not been fully investigated.Here we study how HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121976/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA501870
Series		Accession: GSE121976	ID: 200121976

1057. Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia
(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL20301 188 Samples
FTP download: GEO (BIGWIG, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111015/
Series		Accession: GSE111015	ID: 200111015

1058. Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia [scRNA-seq]
(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for the vast majority of CLL patients. To define the underlining regulatory program, we analyzed high-resolution time courses of ibrutinib treatment in closely monitored patients, combining cellular phenotyping (flow cytometry), single-cell transcriptome profiling (scRNA-seq), and chromatin mapping (ATAC-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111014/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435591
Series		Accession: GSE111014	ID: 200111014

1059. RNA-sequencing of Wnt-dependent and Wnt-independent of Glioblastoma stem cell cultures
(Submitter supplied) Four Wnt-dependent and four Wnt-independent GSC cultures were grown in stem cell media and RNA expression between the two subsets evaluated
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126840/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523440
Series		Accession: GSE126840	ID: 200126840

1060. Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA
(Submitter supplied) The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523366
Series		Accession: GSE126797	ID: 200126797

1061. Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.   The data represent functional transcriptomic profiles of the oncogenic fusion transcription factor EWS/FLI.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122537/
Series		Accession: GSE122537	ID: 200122537

1062. Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI [Experiment 2]
(Submitter supplied) The purpose of this study was to define unique classes of EWS/FLI target genes and the distinct set of structural features present in the EWS domain required for target gene regulation at different EWS/FLI response elements. This study reports the first genome-wide transcriptomic description of a partially-functional EWS/FLI mutant . We report new structure-function dependencies across different classes of response element and tie these dependencies to the ability of EWS/FLI to transform cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 21 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505502
Series		Accession: GSE122536	ID: 200122536

1063. Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI [Experiment 1]
(Submitter supplied) The purpose of this study was to define unique classes of EWS/FLI target genes and the distinct set of structural features present in the EWS domain required for target gene regulation at different EWS/FLI response elements. This study reports the first genome-wide transcriptomic description of a partially-functional EWS/FLI mutant . We report new structure-function dependencies across different classes of response element and tie these dependencies to the ability of EWS/FLI to transform cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 15 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505501
Series		Accession: GSE122535	ID: 200122535

1064. Active ribosome profiling in SETD2 or METTL14 knockdown HepG2 cells
(Submitter supplied) SETD2 is the specific methyltransferase of H3K36me3, while METTL14 is a critical subunit of the m6A methyltransferase complex. To evaluate the effect of SETD2 and METTL14 on translation, we conducted robosome profiling in SETD2 and METTL14 knockdown and control HepG2 cells. Our RNA ribosome profiling revealed that depletion of SETD2 and METTL14 resulted in a global reduction in RNA translation and the changes of translation efficiency were correlated between SETD2 and METTL14 knockdown cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121952/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA501872
Series		Accession: GSE121952	ID: 200121952

1065. RNA stability profiling in SETD2 and METTL14 knockdown HepG2 cells
(Submitter supplied) To evaluate the effect of SETD2 and METTL14 on mRNA stability, we conducted RNA-seq in SETD2 or METTL14 knockdown HepG2 cells as well as control cells with or without actinomycin D treatment. Our RNA stability profiling revealed that depletion of SETD2 and METTL14 resulted in global reduction of RNA stability, and the changes were correlated between SETD2 and METTL14 knockdown cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121949/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA499122
Series		Accession: GSE121949	ID: 200121949

1066. PAR-CLIP-seq of HA-METTL14 in HepG2 cells
(Submitter supplied) The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. To identify METTL14 binding sites in the transcriptome, we overexpressed HA-tagged METTL14 in HepG2 cells and performed PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using HA antibody. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121948/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA499119
Series		Accession: GSE121948	ID: 200121948

1067. RNA-seq analysis of AKTi MK2206 resistant BT474 and T47D cells
(Submitter supplied) BRD4 assembles transcriptional machinery at gene super-enhancer regions and governs the expression of genes that are critical for cancer progression. However, it remains unclear whether BRD4-mediated gene transcription is required for tumor cells to develop drug resistance. Our data show that prolonged treatment of luminal breast cancer cells with AKT inhibitors induces FOXO3a de-phosphorylation, nuclear translocation, and disrupts its association with SIRT6, eventually leading to FOXO3a acetylation as well as BRD4 recognition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118148/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484709
Series		Accession: GSE118148	ID: 200118148

1068. De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization
(Submitter supplied) Common approaches to gene signature discovery in single cell RNA-sequencing depend upon predefined structures like clustering or pseudo-temporal orderings, do not account for the sparsity of single cell data, or require prior normalization.  We present single cell Hierarchical Poisson Factorization (scHPF), a Bayesian factorization method that adapts Hierarchical Poisson Factorization for de novo discovery of both continuous and discrete expression patterns in complex tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116621/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479528
Series		Accession: GSE116621	ID: 200116621

1069. Role of cohesin in cancer development
(Submitter supplied) The aim of this project is to understand the role of cohesin in both genome instability and colorectal cancer development
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113678/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451395
Series		Accession: GSE113678	ID: 200113678

1070. Histone H3 Trimethylation at Lysine 36 (H3K36me3) Guides m6A RNA Modification
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 GPL21103 119 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110323/
Series		Accession: GSE110323	ID: 200110323

1071. Transcriptome stability profiling using 5'-bromouridine IP chase (BRIC-seq) identifies novel and functional microRNA targets in human melanoma cells.
(Submitter supplied) RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126784/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523258
Series		Accession: GSE126784	ID: 200126784

1072. Human prostate cancer cell lines treated with BET Bromodomain inhibitor JQ1
(Submitter supplied) RNA-Sequencing data for DU145 and PC3 cell lines treated with two concentrations of JQ1 in combination with IFN-y to determine effects of BET Bromodomain inhibition on prostate cancer cell lines
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523251
Series		Accession: GSE126779	ID: 200126779

1073. Transcriptomic analysis of the effect of histone H4 K31R mutation in U2OS cells
(Submitter supplied) To explore the genome-wide gene expression changes induced by the K31R mutation in the histone H4 protein, we performed RNA-sequencing analysis in U2OS cells expressing either wildtype H4 or K31R mutant H4. We found that the lysine (K) to arginine (R) mutation mainly affected oxidative phosphorylation, mtiochondria dysfunction and et al, but not DNA damage signaling pathways.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521963
Series		Accession: GSE126451	ID: 200126451

1074. Evidence for HOXC6 as a potential molecular marker for non-small cell lung cancer
(Submitter supplied) HOXC6 is a transcription factor that regulates cell differentiation during embryonic development which is highly expressed in NSCLC, and it may enhance lung cancer progression by regulating the expression of pro-tumorigenic genes involved in proliferation, migration, and invasion. Our study highlighted the oncogenic potential of HOXC6, and suggests that it may be a novel biomarker for the diagnosis and treatment of NSCLC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121896/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA499008
Series		Accession: GSE121896	ID: 200121896

1075. The effect on p53-induced gene transactivation by LIMA1 knockdown.
(Submitter supplied) To explore the effect of LIMA1 on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in LIMA1 knockdown or control A549 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86347/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341491
Series		Accession: GSE86347	ID: 200086347

1076. The effect on p53-induced gene transactivation by NEAT1 knockdown.
(Submitter supplied) To explore the effect of NEAT1 on gene transactivation induced by p53, we evaluated the changes in gene expression by RNA-seq in NEAT1 knockdown or control U2OS cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339519
Series		Accession: GSE85831	ID: 200085831

1077. Potential signaling pathways and gene signatures associated with brain metastases in NSCLC patients
(Submitter supplied) RNA-Seq analyses of various cancers have identified thousands of target genes that help guide clinical treatment. By using RNA-Seq analysis, we examined primary lung tumors from NSCLC patients with and without BM to identify differentially-expressed genes and potential signaling pathways in two groups. A total of 6 patients with histopathologically confirmed NSCLC (against AJCC criteria) were enrolled in the RNA-Seq study, 3 patients with BM and other 3 without BM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126548/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA523020
Series		Accession: GSE126548	ID: 200126548

1078. Characterization of the dynamics of lamin A and lamin B LADs in HepG2 cells: impact of cyclosporin A
(Submitter supplied) Purpose: to qualify and quantify the rearrangement of interactions of nuclear lamins A/C and B with the genome, in relation to nuclearradial  repositioning of loci and changes in gene expression, in HepG2 cells exposed to cyclosporin A. .To compare HepG2 cell line transcriptome profiling (RNA-seq) with radially positioning of the chromatin anchored at the nuclear periphery before and after CsA treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (BED, BEDGRAPH, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119631/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489793
Series		Accession: GSE119631	ID: 200119631

1079. Destabilization of AETFC through C/EBPalpha-mediated repression of LYL1 contributes to t(8;21) leukemic cell differentiation
(Submitter supplied) In t(8;21) leukemic cells, the leukemogenic fusion protein AML1-ETO is stabilized and functions through the AML1-ETO-containing transcription factor complex (AETFC). Destabilization of AETFC thus provides a strategy to target AML1-ETO. In this study, we found that AETFC can be destabilized by a specific mechanism involving a direct repression of the core component LYL1 by C/EBPalpha at transcriptional level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114642/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472044
Series		Accession: GSE114642	ID: 200114642

1080. Comparison of single hWJSCs and hBMMSCs
(Submitter supplied) The Wharton’s jelly of the human umbilical cord contains a population of mesenchymal stem cells that are unique and possess significant clinical utility. Known as human Wharton’s jelly stem cells (hWJSCs), they have broad differentiation potential, are proliferative and available in large numbers from discarded cords thus requiring minimum ex vivo expansion. They are safe and non-tumorigenic and maintain stemness properties for prolonged periods in culture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 161 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110791/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434566
Series		Accession: GSE110791	ID: 200110791

1081. A novel fate-mapping approach allows intratumoral profiling of hypoxic cells
(Submitter supplied) We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Tumors were resected 2 weeks post-implantation, mechanically disrupted and digested with collagenase to obtain a cell suspension. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126609/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522692
Series		Accession: GSE126609	ID: 200126609

1082. An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Human gammaherpesvirus 8
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL25719 17 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126603/
Series		Accession: GSE126603	ID: 200126603

1083. RNA sequencing analysis to identify gene targets of Kaposi's sarcoma herpesvirus (KSHV) ORF24
(Submitter supplied) ORF24 is the core component of a virally encoded transcription complex in KSHV that is active during later stages of infection. ORF24 makes interactions with both promoter DNA and host RNA polymerase II. The aim of this study was to identify the targets of the virally encoded transcription complex by sequencing total RNA from cells that express a mutant ORF24 that does not interact with RNA polymerase II and compare it to RNA from a mutant rescue cell line (WT). more...
Organism:	Human gammaherpesvirus 8; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL25719 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522743
Series		Accession: GSE126602	ID: 200126602

1084. VenomSeq - 25 venoms vs. IMR-32
(Submitter supplied) We report the perturbational effects of 25 crude venoms on human IMR-32 (neuroblastoma) cells. These data are used to evaluate the VenomSeq transcriptomic data analysis workflow, and to provide the first dataset generated by this workflow. By comparison with data published by the Connectivity Map team, and other free sources of genetic perturbation in the context of disease or drug exposure, we use these data to discover several novel associations between venoms and specific therapeutic actions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 192 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126575/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522424
Series		Accession: GSE126575	ID: 200126575

1085. Heterozygous and homozygous knock-in of PIK3CA-H1047R into human iPSCs
(Submitter supplied) We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles of a wild-type induced pluripotent stem cell (iPSC) line (WTC11; Coriell # GM25256; P37-P38). Three clones from each genotype (wild-type, heterozygous, homozygous) were subjected to single-end mRNA sequencing (mean read depth per sample: 20 million) to determine whether PIK3CA-H1047R exerts allele dose-dependent transcriptional effects. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126562/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522373
Series		Accession: GSE126562	ID: 200126562

1086. Rorc disruption in human FG pancreatic cancer cells
(Submitter supplied) Rorc disruption in human FG pancreatic cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522288
Series		Accession: GSE126537	ID: 200126537

1087. Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes
(Submitter supplied) The perivascular niche (PVN) plays an essential role in brain tumor stem-like cell (BTSC) fate control, tumor invasion, and therapeutic resistance. We use a microvasculature-on-a-chip system as a PVN model to evaluate the ex vivo dynamics of BTSCs from ten glioblastoma patients. BTSCs were found to preferentially localize in the perivascular zone, where they exhibited either the lowest motility, as in quiescent cells, or the highest motility, as in the invasive phenotype, with migration over long distance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125587/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516881
Series		Accession: GSE125587	ID: 200125587

1088. Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes
(Submitter supplied) Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126504/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522246
Series		Accession: GSE126504	ID: 200126504

1089. Specific inhibition of splicing factor activity by decoy RNA oligonucleotides
(Submitter supplied) Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126503/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA522237
Series		Accession: GSE126503	ID: 200126503

1090. Comparing Wilms tumor primary samples to patient-derived xenografts
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by array
Platforms: GPL23976 GPL23126 113 Samples
FTP download: GEO (CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110699/
Series		Accession: GSE110699	ID: 200110699

1091. The ALK downregulated target gene HBP1 and repressor of MYCN activity as synergistic target for combined PI3K/HDAC inhibition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL14550 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95193/
Series		Accession: GSE95193	ID: 200095193

1092. The ALK downregulated target gene HBP1 and repressor of MYCN activity as synergistic target for combined PI3K/HDAC inhibition [RNA-Seq]
(Submitter supplied) ALK mutations occur in 10% of primary neuroblastoma and represent a major target for precision treatment. In combination with MYCN amplification, ALK mutations infer an ultra-high-risk phenotype with very poor prognosis. To anticipate to future precision drugging, a deeper understanding of the molecular consequences of constitutive ALK signaling and its relationship to MYCN activity in this aggressive pediatric tumor, will be essential to understand treatment responses and failure as well as to ensure improved design of drugging combinations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376391
Series		Accession: GSE95189	ID: 200095189

1093. Gene expression analysis of a subcutaneous MV4;11 tumor treated with curaxin CBL0137.
(Submitter supplied) The aim of this experiment was to identify how CBL0137 decreased tumor growth in a subcutaneous MV4;11 xenograft model by investigating the gene expression changes induced upon treatment.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL22245 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126442/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521944
Series		Accession: GSE126442	ID: 200126442

1094. Long non-coding RNA expression profile associated with malignant progression of oral submucous fibrosis
(Submitter supplied) Oral submucous fibrosis (OSF) as one of the malignant disorders endures a series of histopathological stages to invasive oral squamous cell carcinoma (OSCC) eventually. The role of long non-coding RNA (lncRNA) expression in OSF malignant progression is still poorly understood. Genome-wide lncRNA expression profiling of normal mucous, OSF and OSCC tissues was performed by RNA sequencing. Bioinformatic methods were applied for differential lncRNA analysis and functional enrichment analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20795 18 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517729
Series		Accession: GSE125866	ID: 200125866

1095. Virus-specific memory T cells populate tumors and can be repurposed for tumor immunotherapy
(Submitter supplied) Improvements in cancer immunotherapy are needed. The immunosuppressive tumor microenvironment limits the success of current immunotherapies. The host retains memory T cells specific for previous infections throughout the entire body that are capable of executing potent and immediate immunostimulatory functions. Here we show that virus-specific memory T cells extend their surveillance to mouse and human tumors. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 34 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512856
Series		Accession: GSE124620	ID: 200124620

1096. Next Generation Sequencing Facilitates Quantitative Analysis of Ramos and Rituximab-resistant Ramos cell Transcriptomes
(Submitter supplied) The goal of this study is to screen the differential genes between Ramos and Rituximab-resistant Ramos cells, then analyze the significant pathways.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112592/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448419
Series		Accession: GSE112592	ID: 200112592

1097. Endometrial epithelial cell transcriptome response to co-culture with adipose stromal cells
(Submitter supplied) The role of obesity in endometrial cancer development is tested by co-culturing adipose stromal cells (ASCs) with endometrial epithelial cells and endometrial cancer cell Ishikawa for 21 days. Control cells (not exposed to ASCs) were incubated for the same duration.  RNA-seq identified differential expression due to ASC exposure
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103203/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400484
Series		Accession: GSE103203	ID: 200103203

1098. The contribution of adenosine receptor 3-mediated signaling to TLR4-induced responses by human dendritic cells
(Submitter supplied) Human dendritic cells were exposed to LPS, in the absence and presence of adenosine receptor 3 inhibitor
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125747/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517436
Series		Accession: GSE125747	ID: 200125747

1099. Human colon organoids reveal distinct physiologic and oncogenic Wnt responses II
(Submitter supplied) Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516869
Series		Accession: GSE125578	ID: 200125578

1100. Human colon organoids reveal distinct physiologic and oncogenic Wnt responses
(Submitter supplied) Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125472/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516452
Series		Accession: GSE125472	ID: 200125472

1101. 3'-TARGET-seq: a novel method for high-sensitivity single-cell mutational analysis and parallel high throughput RNA-sequencing [Figures 5 and 6, Figure S7]
(Submitter supplied) We developed 3'-TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with high throughput 3'-biased whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of 2798 Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with JAK2-V617F mutant myelofibrosis and normal controls using 3'-TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2798 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122198/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503903
Series		Accession: GSE122198	ID: 200122198

1102. Cell type-dependent control of enhancer and p53 transcriptional activity by p63
(Submitter supplied) In this work, we demonstrate that the p53-induced transcriptome is dependent on pre-establishment of cell type-dependent cis-regulatory networks. The epithelial-specific p53 transcriptome is strongly dependent on p63, which acts as a pioneer factor for epithelial-specific enhancers. These results suggest a broad mechanism for regulating the p53-dependent cellular response to stress through differential regulation of cis-regulatory elements and identify p63 as a direct and critical regulator of enhancer activity in epithelial cell types.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 98 Samples
FTP download: GEO (BED, BEDGRAPH, BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111009/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435584
Series		Accession: GSE111009	ID: 200111009

1103. siRNA-mediated silencing of ORAI3 in MDA-MB-468 breast cancer cells exposed to hypoxia
(Submitter supplied) Analysis of the effect of siRNA-mediated silencing of ORAI3 in MDA-MB-468 basal-like breast cancer cells exposed to 48 and 72 h hypoxia
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107692/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421090
Series		Accession: GSE107692	ID: 200107692

1104. Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]
(Submitter supplied) We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 458 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105452/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415205
Series		Accession: GSE105452	ID: 200105452

1105. TARGET-seq: novel method for single-cell mutational analysis and parallel RNA-sequencing [validation in cell lines; Figure 2 and Figure S3]
(Submitter supplied) We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome analysis of JURKAT, SET2 and HSPCs using SMART-seq+, mRNA targeting (tSMARTseq) or TARGET-seq reveals very good correlations between methods.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 180 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415204
Series		Accession: GSE105451	ID: 200105451

1106. The CDK7 Inhibitor THZ1 Alters RNA Polymerase Dynamics at the 5’ and 3’ Ends of Genes
(Submitter supplied) The t(8;21) is one of the most frequent chromosomal translocations associated with acute myeloid leukemia (AML). We found that t(8;21) AML were extremely sensitive to THZ1, which triggered apoptosis after only 4 hr. We used precision nuclear run-on transcription sequencing (PROseq) to define the global effects of THZ1 and other CDK inhibitors on RNA polymerase II dynamics. Inhibition of CDK7 using THZ1 caused wide-spread loss of promoter-proximal paused RNA polymerase. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL18573 42 Samples
FTP download: GEO (BEDGRAPH, DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102243/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397075
Series		Accession: GSE102243	ID: 200102243

1107. Catalytic subunits switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110450/
Series		Accession: GSE110450	ID: 200110450

1108. Catalytic subunits switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells [RNA-seq]
(Submitter supplied) The SWI/SNF chromatin remodeling complex is altered in ~20% of human cancers.  ARID1A, a component of the SWI/SNF chromatin-remodeling complex, is the most frequently mutated epigenetic regulator in human cancers. Inactivation of the SWI/SNF complex is synthetically lethal with inhibition of EZH2 activity.  EZH2 inhibitors are entering clinical trials for specific tumor types with SWI/SNF mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110449/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433734
Series		Accession: GSE110449	ID: 200110449

1109. Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 32 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99544/
Series		Accession: GSE99544	ID: 200099544

1110. Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly [Gro-Seq]
(Submitter supplied) Detailed analysis of estrogen mediated enhancer landscape and chromosomal architectural changes specifically in human chromosome 21.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99539/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388876
Series		Accession: GSE99539	ID: 200099539

1111. A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities.
(Submitter supplied) Development of a novel CRISPR-derived cell line which is a derivative of CWR22Rv1 cells, called CWR22Rv1-AR-EK, that has lost expression of FL-AR, but retains all endogenous AR-Vs. AR-Vs act unhindered by loss of FL-AR to drive cell growth and expression of androgenic genes. Global transcriptomics demonstrate that AR-Vs drive expression of a cohort of DNA damage response genes and depletion of AR-Vs sensitizes cells to ionizing radiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126306/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521519
Series		Accession: GSE126306	ID: 200126306

1112. Exploring the effects of different sample preparation factors on RNA sequencing
(Submitter supplied) We investigated the effects of different sample preparation factors on RNA-seq experiments, including RNA concentration, library storage time, and cryopreserved condition, by comparing their sequencing biases, gene expression profiles, and biological function using primary B cell and CD4+ cell blood samples in healthy subjects.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110417/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433678
Series		Accession: GSE110417	ID: 200110417

1113. A pathogenic CtBP1 missense mutation causes altered cofactor binding and transcriptional activity
(Submitter supplied) We previously reported a pathogenic de novo W342 mutation in the transcriptional corepressor CtBP1 in four independent patients with neurodevelopmental disabilities.  Here, we report the clinical phenotypes of seven additional individuals with the same recurrent de novo CtBP1 mutation.  Within this cohort we identified consistent CtBP1-related phenotypes of intellectual disability, ataxia, hypotonia and tooth enamel defects present in all patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521403
Series		Accession: GSE126253	ID: 200126253

1114. UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93759/
Series		Accession: GSE93759	ID: 200093759

1115. UBR7 is a novel E3 ubiquitin ligase for H2BK120 and acts as a tumor-suppressor in breast cancer [RNA-Seq]
(Submitter supplied) Plant Homeo Domain (PHD) is a versatile chromatin reader/effector module which recognizes methylated, acetylated or unmodified histone substrates and regulates cellular gene expression programs. Although PHD domains shows selective epigenetic recognition of methylated, acetylated and unmodified histone substrates, there has been no previous report on its catalytic function regulating malignant transformation of cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93758/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362305
Series		Accession: GSE93758	ID: 200093758

1116. Transcriptional changes associated with overexpression of TBX3 isoforms (TBX3iso1 and TBX3iso2) in the DCIS-like 21NT cell line
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL5082 18 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126156/
Series		Accession: GSE126156	ID: 200126156

1117. Transcriptional changes associated with overexpression of TBX3 isoforms (TBX3iso1 and TBX3iso2) in the DCIS-like 21NT cell line (RNA-Seq)
(Submitter supplied) Purpose: The acquisition of cellular invasiveness of breast epithelial cells and subsequent transition from ductal carcinoma in situ (DCIS) to invasive breast cancer is a critical step in breast cancer progression. Very little is known about the molecular dynamics governing this transition. We have previously shown that overexpression of the transcriptional regulator TBX3 in DCIS-like 21NT cells results in increased survival, growth, and invasiveness. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126153/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521161
Series		Accession: GSE126153	ID: 200126153

1118. RNA-seq after KD or OE of circRNAs or linear gene
(Submitter supplied) The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-Seq on 144 tumours with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 16 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123940/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510354
Series		Accession: GSE123940	ID: 200123940

1119. Widespread and Functional RNA Circularization in Localized Prostate Cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL20795 GPL11154 63 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113124/
Series		Accession: GSE113124	ID: 200113124

1120. Overexpression and knockdown experiment for circCSNK1G3
(Submitter supplied) Standard RNA analyses using microarrays and low-coverage polyadenylation enriched RNA-Sequencing (RNA-Seq) cannot fully characterize the complexity of the cancer transcriptome. To fully elucidate the transcriptome of prostate tumours, we performed ultra-deep total RNA-Seq on 144 localized prostate tumours with long-term clinical follow up. Analysis of linear RNAs identified a transcriptomic subtype associated with the aggressive intraductal carcinoma subhistology, and a fusion gene profile that differentiates localized from metastatic prostate cancers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113121/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450076
Series		Accession: GSE113121	ID: 200113121

1121. Transcriptome Analysis Reveals a Role for Myc in Constitutive and Antiestrogen-resistant Proliferation of Breast Cancer Cells Expressing ERαY537S and ERαD538G Mutations
(Submitter supplied) Approximately 30% of metastatic breast cancers harbor estrogen receptor α (ERα/ESR1) mutations that are associated with resistance to endocrine therapy and shorter patient survival. How these ERα mutations elicit an aggressive tumor phenotype was largely unknown. Recently, we reported cell lines in which the wild-type ESR1 gene is replaced by the two most common ERα mutations, ERαY537S and ERαD538G. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423078
Series		Accession: GSE108304	ID: 200108304

1122. Expression profiling of histone deacetylase (HDAC) family member genes in human synovial sarcoma cells
(Submitter supplied) We applied RNA sequencing to generate gene expression profiles for human synovial sarcoma SYO-1 and Yamato-SS cells. We particularly focused on eleven histone deacetylase (HDAC) family genes, and found that HDAC1 and -2 are consistently expressed at relatively higher levels in both two cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126152/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521158
Series		Accession: GSE126152	ID: 200126152

1123. Improving fibroblast characterization using single-cell RNA sequencing: an optimized tissue disaggregation and data processing pipeline
(Submitter supplied) Single-cell RNA sequencing (scRNA-Seq) provides a valuable platform for characterising multicellular ecosystems. Fibroblasts are a heterogeneous cell type involved in many physiological and pathological processes, but remain poorly-characterised. Analysis of fibroblasts is challenging: these cells are difficult to isolate from tissues, and are therefore commonly under-represented in scRNA-seq datasets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA521040
Series		Accession: GSE126111	ID: 200126111

1124. Genome-wide maps of chromatin state and gene expression in control and TPA-stimulated pre-B leukemic 697 line
(Submitter supplied) Linker histone H1 has been correlated with transcriptional inhibition, but the mechanistic basis of the inhibition and its reversal during gene activation has remained enigmatic. We report that H1-compacted chromatin, reconstituted in vitro, blocks transcription by abrogating core histone modifications by p300 but not activator and p300 binding. Transcription from H1-bound chromatin is elicited by H1 chaperone NAP1, which is recruited in a gene-specific manner through direct interactions with activator-bound p300 that facilitate core histone acetylation (by p300) and concomitant eviction of H1 and H2A/H2B. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126083/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520988
Series		Accession: GSE126083	ID: 200126083

1125. RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (RNA-Seq)
(Submitter supplied) Mutations in the RUNX1 gene (RUNX1mut) have been established in myelodysplasia (MDS), de novo and secondary acute myeloid leukaemia (AML), and are in general associated with an unfavourable clinical outcome. Familial RUNX1 mutations are associated with familial thrombocytopenia and these patients have a predisposition to AML development. However, a number of studies have been performed so far in mice which might be distinct from the human hematopoietic system. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (BW, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111918/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438539
Series		Accession: GSE111918	ID: 200111918

1126. Neutrophils Escort Circulating Tumor Cells to Enable Cell Cycle Progression
(Submitter supplied) Circulating tumor cells (CTCs) are precursors of metastasis in several cancer types, and are occasionally found within the bloodstream in association with non-malignant cells such as white blood cells (WBCs). The identity and function of these CTC-associated WBCs, as well as the molecular features that define the interaction between WBCs and CTCs are unknown. Here, we achieve the isolation and interrogation of individual CTC-associated WBCs, alongside with corresponding cancer cells within each CTC-WBC-cluster, from multiple breast cancer patients and mouse models.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 GPL19415 470 Samples
FTP download: GEO (RDS, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109761/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431985
Series		Accession: GSE109761	ID: 200109761

1127. quanTIseq: quantifying immune contexture of human tumors
(Submitter supplied) We introduce quanTIseq, a method to quantify the tumor immune contexture, determined by the type and density of tumor-infiltrating immune cells. quanTIseq is based on a novel deconvolution algorithm for RNA sequencing data that was validated with independent data sets. Complementing the deconvolution output with image data from tissue slides enables in silico multiplexed immunodetection and provides an efficient method for the immunophenotyping of a large number of tumor samples.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107572/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420735
Series		Accession: GSE107572	ID: 200107572

1128. RNA-sequencing of formalin fixed human primary melanoma tissue
(Submitter supplied) We identify the differences in nervous system related genes and pathways inside melanoma and in the tissure adjacent to melanoma tumor.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126076/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA520916
Series		Accession: GSE126076	ID: 200126076

1129. Widespread transposable element-driven oncogene expression in cancers
(Submitter supplied) Transposable elements act as promiscuous cryptic promoters that upregulate oncogenes (“onco-exaptation”) in many cancers.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BEDGRAPH, BIGWIG, COV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454575
Series		Accession: GSE113946	ID: 200113946

1130. JAK1/2 inhibitor therapy-associated lymphomas in myelofibrosis arising from a pre-existing B-cell clone
(Submitter supplied) In this study, we elucidated differential gene expression between transformed and untransformed murine Stat1 -/- B cells by RNA sequencing. In addition, clinical samples from 2 lymphoma patients were analyzed. Key results are that 1) JAK1/2 inhibitor treatment in myelofibrosis is associated with an increased risk for aggressive B-cell lymphomas and 2) patients at risk can be identified by screening for pre-existing B-cell clones in peripheral blood or bone marrow.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110219/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433197
Series		Accession: GSE110219	ID: 200110219

1131. Next Generation Sequencing Facilitated Differential Transcriptome Study of melanoma cells transduced with Notch 1 Intracellular Domain (NICD)
(Submitter supplied) Transcriptome profiling (mRNA-seq) of melanoma cells overexpressing NICD
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110179/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433021
Series		Accession: GSE110179	ID: 200110179

1132. Gene expression profiles in response to proanthocyanidins in pancreatic cancer cells
(Submitter supplied) Proanthocyanidins (PAs) that are naturally occurring compounds have shown the potential chemopreventive efﬁcacy against various forms of cancers in different tumor models. To elucidate the responsible molecular mechanisms involved in antitumor therapeutic effects of PAs, the transcriptome changes of pancreatic cancer cells exposure to PAs at 3, 12 and 24h were investigated in this study. Through two biological replicate sequencing, 966, 3543 and 4944 differentially expressed genes in response to PAs exposure were detected at 3, 12 and 24h, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338947
Series		Accession: GSE85610	ID: 200085610

1133. MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors
(Submitter supplied) Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. We screened several MRT cell lines each with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers.  We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin and ATSP-7041, we show that MRT cells are more sensitive than other p53 wild-type cancer cell lines to MDM2 and dual MDM2/4 inhibition in vitro. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124508/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512247
Series		Accession: GSE124508	ID: 200124508

1134. CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary (II)
(Submitter supplied) Inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120298/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492456
Series		Accession: GSE120298	ID: 200120298

1135. CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in hypercalcemic small cell carcinoma of the ovary (I)
(Submitter supplied) Inactivating mutations in SMARCA4 (BRG1), a key SWI/SNF chromatin remodelling gene, underlie small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). To reveal its druggable vulnerabilities, we perform kinase-focused RNAi screens and uncover that SMARCA4-deficient SCCOHT cells are highly sensitive to the inhibition of cyclin-dependent kinase 4/6 (CDK4/6). SMARCA4 loss causes profound downregulation of cyclin D1, which limits CDK4/6 kinase activity in SCCOHT cells and leads to in vitro and in vivo susceptibility to CDK4/6 inhibitors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120297/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492454
Series		Accession: GSE120297	ID: 200120297

1136. Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability (LNCaP RNA-seq)
(Submitter supplied) Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties.  RNA-seq analysis revealed that ABBV-744 elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118152/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484716
Series		Accession: GSE118152	ID: 200118152

1137. Identification of Novel Regulatory Genes in APAP Induced Hepatocyte Toxicity by a Genome-Wide CRISPR-Cas9 Screen
(Submitter supplied) Acetaminophen (APAP) is a commonly used analgesic responsible for more than half of acute liver failure cases. Identification of previously unknown genetic risk factors would provide mechanistic insights and novel therapeutic targets for APAP-induced liver injury. This study used a genome-wide CRISPR-Cas9 screen to evaluate genes that are protective against, or cause susceptibility to, APAP-induced liver injury. more...
Organism:	Escherichia coli; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20045 GPL18460 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA447595
Series		Accession: GSE112463	ID: 200112463

1138. RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer
(Submitter supplied) BACKGROUND: We characterized the whole transcriptome of circulating tumor cells (CTCs) in Stage II-III breast cancer to evaluate correlations with primary tumor biology. METHODS: CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE-FACS). CTCs, PB and fresh tumors were profiled with RNA Seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA Seq and NanoString PAM50 assays with Risk of Recurrence (ROR) scores. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111842/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438345
Series		Accession: GSE111842	ID: 200111842

1139. Tyrosine kinase c-Abl couples RNA polymerase II transcription to an RNA-dependent DNA damage response
(Submitter supplied) Various modes of DNA repair counteract genotoxic DNA double-strand breaks (DSBs) to maintain genome stability. Recent findings suggest that the human DNA damage response (DDR) utilises damage-induced small RNA for efficient repair of DSBs. However, production and processing of RNA is poorly understood. Here we show that localised induction of DSBs triggers phosphorylation of RNA polymerase II (RNAPII) on carboxy-terminal domain (CTD) residue tyrosine-1 in an Mre11-Rad50-Nbs1 (MRN) complex-dependent manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96825/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379827
Series		Accession: GSE96825	ID: 200096825

1140. RNA sequencing of uveal melanona cells treated with VS-4718
(Submitter supplied) To identify dysregulated genes in response to short-term FAK inhibition in uveal melanoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA518896
Series		Accession: GSE126007	ID: 200126007

1141. CircZKSCAN1 suppresses stemness in hepatocellular carcinoma (HCC) by competing against RNA-binding protein FMRP
(Submitter supplied) We found that Quaking5 protein, a RNA splicing protein was downregulated in HCC. Collectively, this study uncovers the mechanisms underlying the regulating role of circZKSCAN1 in HCC cancer stem cells and reveals that the new discovered Qki5-circZKSCAN1-FMRP-CCAR1-Wnt signaling axis is of important therapeutic value in improving the treatment of HCC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432661
Series		Accession: GSE110048	ID: 200110048

1142. Searching for target genes of miR-508/509/506/514 in HCT116 cells
(Submitter supplied) To elucidate whether miR-508/508/509/514  plays a role in colorectal cancer tumorigenesis,  RNA-seq analysis was performed to compare the gene expression profiles of miR-508/508/509/514 mimics and control microRNA transfectants.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 14 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77462/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310425
Series		Accession: GSE77462	ID: 200077462

1143. GOYA DLBCL clinical trial - RNASeq dataset
(Submitter supplied) This dataset contains collected RNASeq data of 552 samples from the GOYA clinical trial.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 553 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA518119
Series		Accession: GSE125966	ID: 200125966

1144. Antagonism of IAPs enhances CAR T cell efficacy
(Submitter supplied) Chimeric antigen receptor (CAR) T cell therapy has proven highly successful in the treatment of hematological malignancies, notably acute lymphoblastic leukemia and B cell lymphoma. However, the efficacy of CAR T cells against solid tumors is poor, likely due to tumor-associated immunosuppression. Here, we demonstrate that antagonizing Inhibitor of Apoptosis Proteins (IAPs) with the clinical smac-mimetic, birinapant, significantly enhanced the anti-tumor activity of CAR T cells in a TNF-dependent manner. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124140/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510825
Series		Accession: GSE124140	ID: 200124140

1145. Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers
(Submitter supplied) Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC). In vitro, TS knockdown increased the population of CD24+ differentiated cells, and attenuated migration and sphere-formation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122953/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506989
Series		Accession: GSE122953	ID: 200122953

1146. Gene expression profiles of BxPC-3, MiaPaCa-2 and PANC-1 cell lines treated with DMSO and THZ1 respectively
(Submitter supplied) By screening an epigenetic-related compound library, we identified THZ1, a covalent inhibitor of CDK7, as a promising candidate. Multiple long-established and patient-derived PDAC cell lines (PDC) were used to validate the efficacy of THZ1 in vitro. In addition, patient-derived xenograft (PDX) models and animal models of PDAC were utilized for examining THZ1 efficacy in vivo. Furthermore, RNA-Seq and H3K27Ac-based Super-Enhancers (SEs) analyses were performed to reveal the molecular mechanism of THZ1 treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496574
Series		Accession: GSE121273	ID: 200121273

1147. Transcriptomic analysis of the RPS3-regulated genes in HCC cell line
(Submitter supplied) The human ribosomal protein S3 (RPS3), a component of the small 40S ribosomal subunit, is mainly involved in ribosomal maturation and initiation of translation through association with initiation factors. In this study, we firstly identified that RPS3 played an important role in HCC progression. We performed RNA sequencing to profile gene expression patterns before and after RPS3 knockdown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118140/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484691
Series		Accession: GSE118140	ID: 200118140

1148. A code of mono-phosphorylation modulates the function of RB.
(Submitter supplied) Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB’s interactions and confer functional specificity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116346/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478228
Series		Accession: GSE116346	ID: 200116346

1149. Comparison of the differentially expressed genes in normal vs ovarian cancer cells
(Submitter supplied) Identification of the differentially expressed genes in the cancer cells (mainly focusing on the growth factor receptors)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109981/
Series		Accession: GSE109981	ID: 200109981

1150. Nicotinamide Nucleotide Transhydrogenase as a novel treatment target in adrenocortical carcinoma
(Submitter supplied) RNA-seq samples used to support a study in to the understanding of antioxidant targeting in adrenocortical carcinoma
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418300
Series		Accession: GSE106873	ID: 200106873

1151. Distinct gene expression profile of Huh7 cell lines stably overexpressing CRABP1 or 2
(Submitter supplied) The metabolism of ROL to the biogenesis of ATRA occurs in the cytoplasms of hepatocytes, which in turn translocates into nucleus upon binding to Cellular Retinoic Acid Binding Proteins, CRABP1 or CRABP2. However, the differential effect of CRABP1 and CRABP2 on the intracellular environment is not well understood.  Here,  we report polyA RNA sequencing data of the CRABP1 or CRABP2 overexpressing Huh7 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101934/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395976
Series		Accession: GSE101934	ID: 200101934

1152. Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 9 Samples
FTP download: GEO (DIFF, FPKM_TRACKING, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94545/
Series		Accession: GSE94545	ID: 200094545

1153. Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma [RNA-Seq]
(Submitter supplied) Epigenetic modifications in the form of altered DNA or histone methylation can influence gene expression patterns critical for neoplastic initiation and progression. The fact that abnormal gene expression can be driven by epigenetic alterations led us to examine the correlation between DNA methylation, trimethylation of histone 3 lysine 9 (H3K9me3) and lysine 27 (H3K27me3), and gene expression in esophageal adenocarcinoma (EAC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (DIFF, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94544/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371455
Series		Accession: GSE94544	ID: 200094544

1154. Mucin 1 knockdown in EMM myeloma cells
(Submitter supplied) The sialic glycoprotein, Mucin1, is known to be involved in the pathogenesis of various types of cancers. In a fraction of patients with multiple myeloma, their myeloma cells have high Mucin1 expression. We established a myeloma cell line designated EMM1 from a myeloma patient whose myeloma cells have high Mucin1 expression. Then we performed knockdown of Mucin1 to elucidate the role of the high Mucin1 expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114885/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472976
Series		Accession: GSE114885	ID: 200114885

1155. Venetoclax with azacitidine disrupts energy metabolism and targets leukemia stem cells in patients with acute myeloid leukemia
(Submitter supplied) Acute myeloid leukemia (AML) is the most common acute leukemia in adults. Leukemia stem cells (LSCs) drive the initiation and perpetuation of AML, are quantifiably associated with worse clinical outcomes, and often persist after conventional chemotherapy resulting in relapse1-5. In this report, we show that treatment of older patients with AML with the B cell lymphoma 2 (BCL-2) inhibitor venetoclax in combination with azacitidine results in deep and durable remissions and is superior to conventional treatments. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116481/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478784
Series		Accession: GSE116481	ID: 200116481

1156. Transcriptome profiling of HCC1937 vector and wtBRCA1 cell lines which were treated with OTX-015
(Submitter supplied) Purpose: To compare the transcriptomes of HCC1937 vector and wtBRCA1 cells which were treated with OTX-015. Methods: HCC1937 vector and wtBRCA1 cells were treated with 5 micromolar OTX-015 for 24 hours. Total RNA was extracted and processed with NEBNext Ultra Directional RNA Library Prep Kit for cDNA library preparation. The data are in duplicate and raw data were generated by Illumina 2500 sequencer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109809/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432071
Series		Accession: GSE109809	ID: 200109809

1157. Plasminogen activator inhibitor 1 (PAI1) promotes actin cytoskeleton reorganization and glycolytic metabolism in triple negative breast cancer
(Submitter supplied) We altered the expression of PAI1 in SUM159 breast cancer cell line and would like to see the effects
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125802/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA517541
Series		Accession: GSE125802	ID: 200125802

1158. EIF1AX-A113 splice and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC
(Submitter supplied) Translation initiation in higher eukaryotes is orchestrated by the tight regulation of the cap binding and the 43S pre-initiation complexes (PIC). The PIC component eukaryotic initiation factor 1A (EIF1A), encoded on human chromosomes X and Y by EIF1AX and EIF1AY, respectively, is essential for recruitment of the ternary complex and for assembling the 43S PIC, which after recruitment onto capped mRNAs scans their 5’UTR and localizes the AUG to initiate translation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 18 Samples
FTP download: GEO (FASTA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113695/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453686
Series		Accession: GSE113695	ID: 200113695

1159. mRNA sequence  Analysis of Apocynin treated MKN45
(Submitter supplied) Noxo1, a component of NADPH oxidase 1 (NOX1) complex, is upregulated in gastric cancer cells in a inflammation-dependent manner, and plays an important role in tumorigenesis (Oncogene, 33: 3820, 2014). To examine the mechanism of NOX1/ROS signaling in tumorigenesis, MKN45 gastric cancer cells were treated with apocynin, an inhibitor for NOX, and their gene expression was examined by RNA sequencing. Based on expression data, Sox2 was shown to be suppressed by apocynin, suggesting a role of Sox2 in a inflammation-associated gastric tumorigenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437294
Series		Accession: GSE111520	ID: 200111520

1160. A novel non-canonical signaling pathway mediates TGF-β1-induced glucocorticoid insensitivity in epithelial cells
(Submitter supplied) Limited therapeutic responses to glucocorticoids in chronic inflammatory disease are partly attributable to interleukins and transforming growth factor-β1 (TGF-β1). Global inhibition of TGF-β1 carries known risks, including autoimmune disease.  Here we elucidate the signaling pathway subserving modulation of glucocorticoid activity by TGF-β1. The proteomic response of airway epithelial cells to TGF-β1 revealed 24 candidate proteins of which 3 were prioritized by exclusion of changes induced by: TGF-β2, which lacks the modulatory activity of TGF-β1 and TGF-β3; and those of TGF-β1 that were prevented by small molecule inhibitors of non-canonical TGF-β1 signaling, that did not prevent glucocorticoid modulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104908/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414116
Series		Accession: GSE104908	ID: 200104908

1161. A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
(Submitter supplied) Temozolomide (TMZ) is a frequently used chemotherapy for glioma; however, chemoresistance is a major problem limiting its effectiveness. Thus knowledge of mechanisms underlying this outcome could improve patient prognosis. Here, we report that deletion of a regulatory element in the HOTAIR locus increases glioma cell sensitivity to TMZ and alters transcription of multiple genes. Analysis of a combination of RNA-seq, Capture HiC and patient survival data suggests that CALCOCO1 and ZC3H10 are target genes repressed by the HOTAIR regulatory element and that both function in regulating glioma cell sensitivity to TMZ. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL20795 GPL20301 10 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125629/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516515
Series		Accession: GSE125629	ID: 200125629

1162. Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL15520 GPL18573 8 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109675/
Series		Accession: GSE109675	ID: 200109675

1163. Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [RNA-seq]
(Submitter supplied) Multiple myeloma (MM) is a hematological malignancy caused by accumulation of abnormal clonal plasma cells. Despite the recent development of novel therapies, relapse of MM eventually occurs due to a remaining population of drug-resistant myeloma stem cells. Side population (SP) cells exhibit cancer stem cell-like characteristics in MM; thus targeting these cells is a promising strategy to completely cure this malignancy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109673/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431630
Series		Accession: GSE109673	ID: 200109673

1164. Gene Expression Profiling of Cutaneous CD30+ Lymphoproliferative Disorders by RNA-seq
(Submitter supplied) Cutaneous CD30+ lymphoproliferative disorder (CD30+LPDs), including lymphomatoid papulosis (LyP) and primary cutaneous anaplastic large-cell lymphoma (PCALCL), comprises the second most common group of cutaneous T cell lymphoma. Previously, we reported that special AT-rich sequence-binding protein1 (SATB1), a thymocyte specific chromatin organizer, was over-expressed and promoted malignant T-cell proliferation in a portion of CD30+LPDs, whereas other CD30+LPDs didn't express SATB1 at all. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431541
Series		Accession: GSE109620	ID: 200109620

1165. En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements
(Submitter supplied) RNA-seqs followed by whole and segmental deletions of XIST genes in human K562 cells. The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and the XCI-involving RNA elements remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, ten smaller XIST segments, including repeats A, D, and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and fluorescence in-situ hybridization experiments on XIST RNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL16791 29 Samples
FTP download: GEO (TXT, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65830/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA275148
Series		Accession: GSE65830	ID: 200065830

1166. Gene expression for surgically treated pancreatic cancer after one neoadjuvant vaccine dose
(Submitter supplied) RNA seq gene expression analysis of patients with resected pancreatic cancer following 1 dose of GM-CSF expressing whole cell pancreatic vaccine 2 weeks prior to resection. Samples were obtained for IHC analysis of protein expression, IHC analysis of immune cell infitration and RNA sequencing correlates
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516645
Series		Accession: GSE125506	ID: 200125506

1167. RNA-sequencing analysis examining how the Vibrio cholerae MARTX toxin and its inidividual effector domains modulate the transcriptome of human intestinal epithelial cells.
(Submitter supplied) MARTX toxins are large single polypeptide bacterial toxins that translocate multiple cytotoxic and functionally independent effector domains into the cytosol of a target eukaryotic cell. Pandemic Vibrio cholerae El Tor O1 strains secrete a MARTX toxin with three effector domains — the actin crosslinking domain (ACD), the Rho inactivation domain (RID), and the alpha/beta-hydrolase domain (ABH) — to regulate innate immunity and enhance colonization. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516425
Series		Accession: GSE125453	ID: 200125453

1168. Epithelial mesenchymal transition (EMT) in A549 NSCLC cells. TGFbeta was used to induce EMT, RNA isolated and subjected to RNAseq on Illumina HiSeq
(Submitter supplied) The capacity of cancer cells to undergo epithelial mesenchymal trans-differentiation has been implicated as a factor driving metastasis, through the acquisition of enhanced migratory/invasive cell programs and the engagement of anti-apoptotic mechanisms promoting drug and radiation resistance. Our aim was to define molecular signaling changes associated with mesenchymal trans-differentiation in two KRas mutant NSCLC models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515936
Series		Accession: GSE125369	ID: 200125369

1169. Time course of TGFbeta induced epithelial mesenchymal transition (EMT) in H358 NSCLC cells.
(Submitter supplied) The capacity of cancer cells to undergo epithelial mesenchymal trans-differentiation has been implicated as a factor driving metastasis, through the acquisition of enhanced migratory/invasive cell programs and the engagement of anti-apoptotic mechanisms promoting drug and radiation resistance. Our aim was to define molecular signaling changes associated with mesenchymal trans-differentiation in two KRas mutant NSCLC models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515921
Series		Accession: GSE125365	ID: 200125365

1170. LSD1 pharmacological inhibition in SET-2 containing wild type and mutant LSD1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 32 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121426/
Series		Accession: GSE121426	ID: 200121426

1171. LSD1 pharmacological inhibition in SET-2 containing wild type and mutant LSD1 [RNA-Seq]
(Submitter supplied) We characterized the effect of GSK-LSD1 treatment on gene expression for both wt SET-2 and drug-resistant SET-2 LSD1 (Leu659_Asn660insArg)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121425/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497303
Series		Accession: GSE121425	ID: 200121425

1172. Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
(Submitter supplied) We studied global distribution of hydroxymethylation (5hmC) and DNA methylation (5mC) in during normal B-cell development and CLL maturation. To derive disease-specific epigenetic changes we have compared CLL subgroups to their corresponding cell of origin. Our data showed that naïve B-cells, compared to non-class switched and class switched memory B-cells, had higher levels of 5-hmC and 5-mC. By comparing with ChIP sequencing data of H3K27Ac and H3K4me1 modifications of CLL samples with 5hmC and 5mC levels, we observed an increase of 5-hmC at overall gene body regions, CpG island shores and regulatory elements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 82 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113386/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450999
Series		Accession: GSE113386	ID: 200113386

1173. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 36 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113217/
Series		Accession: GSE113217	ID: 200113217

1174. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition [RNA-seq]
(Submitter supplied) Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT or PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, producing high expression levels of the oncogene required for tumor growth. Though kinase inhibition is an effective therapy for many GIST patients, disease progression from kinase resistance mutations is common, and no other efficacious classes of systemic therapy exist. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450436
Series		Accession: GSE113215	ID: 200113215

1175. LINE-2 transposable elements are a source of functional human microRNAs and target sites
(Submitter supplied) Transposable elements (TEs) are dynamically expressed at high levels in multiple human tissues, but the function of TE-derived transcripts remains largely unknown. In this study, we identify numerous TE-derived microRNAs (miRNAs) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (AGO2 RIP-seq) on human brain tissue. Many of these miRNAs originated from LINE-2 (L2) elements, which entered the human genome around 100-300 million years ago. more...
Organism:	Mus musculus; Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL21290 GPL16791 49 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418122
Series		Accession: GSE106810	ID: 200106810

1176. Global transcriptional changes in the JJN3 myeloma cell line that occur as a result of treatment with 2 pyrrolobenzodiazepine (PBD) monomers
(Submitter supplied) Background: This study characterises a group of Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) monomeric hybrids to investigate the global transcriptional changes that occur as a result of treatment in these cells. It was also of interest to determine whether compounds show a selective inhibitory effect on the NF-kB consenus sequence and hence NF-kB signalling. Methods: NF-kB is often overexpressed and over-active in multiple myeloma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA516213
Series		Accession: GSE125395	ID: 200125395

1177. Characterization of RNA context tumor associated macrophages and related extracellular vesicles
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123474/
Series		Accession: GSE123474	ID: 200123474

1178. Characterization of RNA context tumor associated macrophages and related extracellular vesicles [RNA-seq]
(Submitter supplied) Extracellular vesicles (EVs) are membrane vesicles released by all cell types and contain proteins and non-coding RNAs, which are transported into recipient cells to regulate their signal transduction and functions. Increasing evidence has demonstrated that EV shuttling is an effective means of bio-molecule transportation among various cell types in the tumor microenvironment, and thus plays a critical role in regulating cancer cell biology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508813
Series		Accession: GSE123471	ID: 200123471

1179. Promoter-proximal pausing mediated by the exon junction complex regulates splicing
(Submitter supplied) Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 142 Samples
FTP download: GEO (BW, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92389/
Series		Accession: GSE92389	ID: 200092389

1180. RNA-seq of nine primary human cell types exposed in vitro to methylprednisolone
(Submitter supplied) Glucocorticoids remain the most widely used class of anti-inflammatory and immunosuppressive agents. They act primarily by binding to the glucocorticoid receptor, resulting in direct and indirect effects on gene expression. The current understanding of glucocorticoid effects on transcription in human cells is based mostly on studies of cancer cell lines, immortalized cell lines, or highly mixed populations of primary cells (such as peripheral blood mononuclear cells). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21290 GPL11154 144 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112101/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA439288
Series		Accession: GSE112101	ID: 200112101

1181. Small-molecule targeting of brachyury transcription factor addiction in chordoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 16 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121846/
Series		Accession: GSE121846	ID: 200121846

1182. Small-molecule targeting of brachyury transcription factor addiction in chordoma [rnaseq_sgrna]
(Submitter supplied) Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121845/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498627
Series		Accession: GSE121845	ID: 200121845

1183. Small-molecule targeting of brachyury transcription factor addiction in chordoma [rnaseq_compound]
(Submitter supplied) Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121843/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498620
Series		Accession: GSE121843	ID: 200121843

1184. Small-molecule targeting of brachyury transcription factor addiction in chordoma [ATAC-Seq]
(Submitter supplied) Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432041
Series		Accession: GSE109785	ID: 200109785

1185. ESRP1 knockdown in breast cancer cells
(Submitter supplied) ESRP1 was knocked down in endocrine resistant LCC2 and LCC9 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (FPKM_TRACKING, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125355/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515910
Series		Accession: GSE125355	ID: 200125355

1186. SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL21290 GPL16686 28 Samples
FTP download: GEO (BEDGRAPH, BIGWIG, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125334/
Series		Accession: GSE125334	ID: 200125334

1187. Identify novel TGF-β-regulated genes by RNA-sequencing from MCF10A cells
(Submitter supplied) TGF-β signaling and its induced EMT (Epithelial to mesenchymal transition) play fundamental roles in development and disease including cancers. Although, TGF-β-regulated genes have been extensively studied, with RNA-sequencing (RNA-seq) analysis, new TGF-β-regulated genes are still been identified. Moreover, many significantly regulated genes by TGF-β are not emphasized. This study employs RNA-seq on MCF10A cells treated by TGF-β for 1.5 (this GEO), 24, 48, and 72 (GSE74377) hours and aims to identify novel TGF-β-regulated genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125280/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515740
Series		Accession: GSE125280	ID: 200125280

1188. Compare of gene expression between p16INK4A positive and negative regions of colon cancer from five patients
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125253/
Series		Accession: GSE125253	ID: 200125253

1189. Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC346]
(Submitter supplied) To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125252/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515695
Series		Accession: GSE125252	ID: 200125252

1190. Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC173]
(Submitter supplied) To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125251/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515699
Series		Accession: GSE125251	ID: 200125251

1191. Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC100]
(Submitter supplied) To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125250/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515698
Series		Accession: GSE125250	ID: 200125250

1192. Compare of gene expression between p16INK4A positive and negative Colon cancer [2018HC067]
(Submitter supplied) To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125248/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515697
Series		Accession: GSE125248	ID: 200125248

1193. Compare of gene expression between p16INK4A positive and negative Colon cancer [2017HC070]
(Submitter supplied) To evaluate gene expression in an in colon cancer, we analyzed the gene expression profile of p16INK4A positive or negative expressed colon cancer region by RNA sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125247/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515696
Series		Accession: GSE125247	ID: 200125247

1194. A Novel Glioma-specific Enhancer Maintains Glioma Temozolomide Sensitivity By Regulation of RasGRP3 Expression via Long-range Chromosome Interactions
(Submitter supplied) In this study, we report the identification of a glioma-specific enhancer that confers sensitivity to TMZ by upregulation of the mitogen-associated protein kinase activator RasGRP3. Deletion of either the active domain of RasGPR3 or the enhancer using CRISPR/Cas9, was sufficient to restore sensitivity to TMZ in a resistant population of cells that was reversed with overexpression of RasGRP3. The project include RNA-seq, Hi-C, Capture Hi-C between DMSO-treated U251 and TMZ-treated U251.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL20301 GPL20795 12 Samples
FTP download: GEO (MATRIX, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125243/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515368
Series		Accession: GSE125243	ID: 200125243

1195. Targeting EZH2 increases the vulnerability of triple-negative breast cancer
(Submitter supplied) We hypothesize that knockdown or inhibition of the EZH2 results in decreased proliferation and tumorigenic potential of TNBC breast cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 9 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112378/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445854
Series		Accession: GSE112378	ID: 200112378

1196. Prostate Cancer Cell RNA-Seq (PC3E and GS689.Li)
(Submitter supplied) Two prostate cancer cell lines. PC3E and GS689.Li
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL15520 GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112037/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438990
Series		Accession: GSE112037	ID: 200112037

1197. Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids
(Submitter supplied) RNA sequencing technology was applied to determine the transcriptional changes due to palmitate treatment, RNF213 knockdown, and GPAT4 knockdown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125178/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515481
Series		Accession: GSE125178	ID: 200125178

1198. RNA sequencing to determine gene expression changes in HMCES knockout cells
(Submitter supplied) The purpose of this study was to deteremine gene expression changes in when HMCES is inactivated. We found very few changes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121515/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497524
Series		Accession: GSE121515	ID: 200121515

1199. Gene expression analysis of prostate cancer cells treated with fatty acid synthase (FASN) inhibitor IPI-9119
(Submitter supplied) Alterations in gene expression following fatty acid synthase inhibtion were evaluated in androgen sensitive LNCaP cells and castration resistant 22Rv1 and LNCaP-95 cells.  Cell were exposed to 2 concentrations (0.1 and 0.5 uM) of  FASN inhibitor IPI-9119 or DMSO for 6 days.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454882
Series		Accession: GSE114016	ID: 200114016

1200. Lysine specific demethylase 1 inactivation enhances differentiation and promotes cytotoxic response when combined  with all-trans retinoic acid in acute myeloid leukemia across   subtypes
(Submitter supplied) Combined treatment with all-trans retinoic acid and GSK2879552 results in synergistic effects on gene expression, cell proliferation, markers   of differentiation, and, most importantly, cytotoxicity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125112/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515266
Series		Accession: GSE125112	ID: 200125112

1201. Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109246/
Series		Accession: GSE109246	ID: 200109246

1202. Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines (mRNA-Seq)
(Submitter supplied) The goal of the study is to compare NGS-derived transcriptome (mRNA-seq) profiles of melanocytes and metastatic melanoma cells and identify genes involved in melanomagenesis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109245/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430242
Series		Accession: GSE109245	ID: 200109245

1203. Paclitaxel plus Cirmtuzumab Achieves Greater Clearance of Patient-derived Xenografts By Targeting ROR1+ Breast Cancer Stem Cells
(Submitter supplied) We applied  high-throughput sequence to identify signaling pathways, stem cell gene signature or target genes of BMI1 that were affected by our newly development humainzed anti-ROR1 antibody (cirmtuzumab) in breast cancer patient-derived xenograft (PDX) mice model
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427913
Series		Accession: GSE108632	ID: 200108632

1204. Next Generation Sequencing Quantitative Analysis of Wild Type and AML1-ETO Related Fusion Circular RNA (F-CircAE) Knockdown Kasumi-1 Cells Transcriptomes
(Submitter supplied) The goal of this study is to determine the difference in transcriptome expression profils between wild type and AML1-ETO related fusion circular RNA knockdown Kasumi-1 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125043/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA515048
Series		Accession: GSE125043	ID: 200125043

1205. Differetially expressed genes after hTR overexpression in U2OS cells
(Submitter supplied) lncRNA is reported to regulate gene transcription in variety of ways. hTR is a lncRNA with 451 nt. It is classical role is serving as template for telomere lengthening. However, it involves in some other biology processes as a lncRNA. To screen for genes regulated by hTR, we performed RNAseq with hTR expressed U2OS cells, using pBabe-U2OS as control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125024/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514991
Series		Accession: GSE125024	ID: 200125024

1206. Gene expression analysis in response to hypoxic pathway inhibition
(Submitter supplied) Gene expression analysis of HeLa cells exposed to hypoxia (1% Oxygen), treated with a PHD inhibitor (IOX2) or treated with a VHL inhibitor (VH032) for 16 hours
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120675/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494075
Series		Accession: GSE120675	ID: 200120675

1207. Contribution of SRF and Nkx2-5 to androgen-dependent gene expression in prostate cancer
(Submitter supplied) To study and compare the effect of siRNA-mediated SRF or Nkx2-5 silencing on androgen-responsive genes in LNCaP cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116728/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480000
Series		Accession: GSE116728	ID: 200116728

1208. The Role of CD83 in ovarian cancer cell line SKOV3
(Submitter supplied) We performed RNA-Seq of CD83 overexpression SKOV3 cells (OV_1, OV_2, OV_3), CD83 knockdown SKOV3 cells (KD_1, KD_2, KD-3), and control SKOV3 cells (NC_1, NC_2, NC_3) using BGISEQ-500 platform (BGI, China).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125011/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514904
Series		Accession: GSE125011	ID: 200125011

1209. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (RNAseq)
(Submitter supplied) Despite the ever-increasing speed of detecting fusion transcripts in cancer, it remains formidable to predict what unreported RNA pairs can form new fusion transcripts. By systematic mapping of chromatin-associated RNAs (caRNAs) and their respective genomic interaction loci, we obtained genome-wide RNA-DNA interaction maps from two non-cancerous cell types. The gene pairs involved in RNA-DNA interactions in these normal cells exhibited strong overlap with those with cancer-derived fusion transcripts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 70 Samples
FTP download: GEO (FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506022
Series		Accession: GSE122688	ID: 200122688

1210. The mRNA export receptor NXF1 coordinates transcriptional dynamics, alternative polyadenylation and mRNA export
(Submitter supplied) Alternative polyadenylation (APA) produces mRNA isoforms with different 3’UTR lengths. Previous studied indicated that 3’ end processing and mRNA nuclear export are intertwined in gene regulation. Here, we show that mRNA export factors generally facilitate usage of distal cleavage and polyadenylation sites (PASs), leading to expression of long 3’UTR isoforms. By focusing on the export receptor NXF1, which exhibits the most potent effect on APA in this study, we reveal a number of gene features that impact NXF1-dependent APA, including 3’UTR size, gene size and AT content. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL20795 GPL11154 25 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117701/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482996
Series		Accession: GSE117701	ID: 200117701

1211. SWI/SNF Chromatin Remodeling Factor BRG1 is Synthetic Required for PTEN-deficient Prostate Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL20795 GPL20301 9 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115619/
Series		Accession: GSE115619	ID: 200115619

1212. Transcriptome analysis of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation
(Submitter supplied) We conduct transcriptome comparison of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation to gain genomic insights on the biological processes that BRG1 is involved in depend on PTEN deletion.  Through unsupervised cluster analysis of differentially expressed genes (DEGs), we found the expressions of 5489 genes were significantly altered in PTEN/BRG1 double knockdown cells, whereas they remained consistent or opposite pattern in control, BRG1-KD and PTEN-KD cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115616/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475578
Series		Accession: GSE115616	ID: 200115616

1213. Inhibition of SF3B1 by molecules targeting the spliceosome in Rh18 cells
(Submitter supplied) In order to examine the effects of sudemycin D1 on the whole transcriptome, we exposed Rh18 cells to 1μM of drug for 8hr and after extraction, subjected RNA to RNAseq analysis. Control samples were treated with the vehicle (DMSO) alone and all analyses were conducted in triplicate.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102539/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397981
Series		Accession: GSE102539	ID: 200102539

1214. small RNA and mRNA sequencing data of human granulosa cells from PCOS women with insulin resistance
(Submitter supplied) Our objective was to identify the miRNA and mRNA expression profiles in PCOS women with or without insulin resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124968/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514719
Series		Accession: GSE124968	ID: 200124968

1215. Gene expression altered by HOTAIR knockdown in MCF-7-TNR
(Submitter supplied) The human HOTAIR-specific siRNA and control siRNA were transfected into MCF-7-TNR cells. RNA was collected at 72 hrs after transfection. RNA-SEQ was carried out to profile the gene expression altered by HOTAIR knockdown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124934/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA514345
Series		Accession: GSE124934	ID: 200124934

1216. Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data
(Submitter supplied) We perform a large-scale RNA sequencing study to experimentally identify genes that are downregulated by 25 miRNAs. This RNA-seq dataset is combined with public miRNA target binding data to systematically identify miRNA targeting features that are characteristic of both miRNA binding and target downregulation. By integrating these common features in a machine learning framework, we develop and validate an improved computational model for genome-wide miRNA target prediction. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 52 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512378
Series		Accession: GSE124530	ID: 200124530

1217. Genome wide expression change by RNF168 knocking down in NEC cells
(Submitter supplied) We aim to the investigate the role of RNF168 in breast cancer progression. NEC cells were used as the model and RNF168 was silenced by siRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118532/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485964
Series		Accession: GSE118532	ID: 200118532

1218. Circulating Tumor Cells Clustering Triggers DNA Methylation Changes to Enable Metastasis Seeding
(Submitter supplied) The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Our DNA methylation analysis led us to hypothesize that CTC clusters are characterized by active TF networks that support both stemness and proliferation. To identify whether the stemness- and proliferation-related TF networks are also transcriptionally active in CTC clusters compared to single CTCs, we performed single-cell resolution RNA sequencing analysis of single CTCs and CTC clusters, matched within individual liquid biopsies and isolated from six breast cancer patients with progressive metastatic disease, and of single CTCs and CTC clusters isolated from three xenograft models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 210 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435739
Series		Accession: GSE111065	ID: 200111065

1219. RNA-seq of MCF7 spheroids after macrophage infiltration.
(Submitter supplied) To determine effects of primary human macrophages on breast tumor cell mRNA levels, breast carcinoma cell line MCF7 were grown as spheroids in the presence or absence of infiltrating macrophages.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119147/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488257
Series		Accession: GSE119147	ID: 200119147

1220. Activating Transcription Factor 4 modulated TGFb-induced aggresiveness in triple negative breast cancer vis SMAD2/3/4 and mTORC2 signaling
(Submitter supplied) Based on the identified stress-independent cellular functions of activating transcription factor 4 (ATF4), we reported enhanced ATF4 levels in MCF10A cells treated with TGFβ1. ATF4 is overexpressed in triple negative breast cancer (TNBC) patients, but its impact on patient survival and the underlying mechanisms remain unknown. We aimed to determine ATF4 effects on breast cancer patient survival and TNBC aggressiveness, and the relationships between TGFβ and ATF4.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113362/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450921
Series		Accession: GSE113362	ID: 200113362

1221. Global host gene expression changes in KSHV+ PEL cells upon KSHV reactivation
(Submitter supplied) Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic virus, which maintains the persistent infection of the host by intermittently reactivating from latently infected cells to produce viral progenies. Here, we performed a comprehensive time course transcriptome analysis during KSHV reactivation in KSHV+ primary effusion B-cell lymphoma cells (PEL). For this we used a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123898/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510136
Series		Accession: GSE123898	ID: 200123898

1222. Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20301 72 Samples
FTP download: GEO (BEDPE, FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122690/
Series		Accession: GSE122690	ID: 200122690

1223. MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [iCLIP]
(Submitter supplied) We performed iCLIP for AGO2 to identify AGO2-interacting mRNAs in T98G glioblastoma multiforme cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448605
Series		Accession: GSE112651	ID: 200112651

1224. MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network with PRC2 [RNA-seq]
(Submitter supplied) We performed RNA-seq to identify differentially expressed genes in response to knockout of EZH2 and global miRNA knockdown (VP55 overexpressed) in T98G Glioblastoma multiforme cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112241/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445338
Series		Accession: GSE112241	ID: 200112241

1225. The dynamic landscape of coding and non-coding RNAs in the innate immune response to microbial pathogens
(Submitter supplied) We performed a systematic analysis of the coding and non-coding transcriptomes of human macrophages after stimulation with ligands to TLR2/6  (FSL), TLR 1/2  (Pam3CSK4), and TLR4 (LPS)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109084/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429621
Series		Accession: GSE109084	ID: 200109084

1226. The study of the role of POU3F2 in response to UVB treatment
(Submitter supplied) siRNA KD of POU3F2 directly effect DNA-damage repair and apoptosis genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124761/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513348
Series		Accession: GSE124761	ID: 200124761

1227. Quantitative Analysis of negative control and overexpression-TRIB1 in PC3 and DU145 Transcriptomes
(Submitter supplied) The goals of this study is to find effect of overexpression-TRIB1 to prostate cancer cell (PC3 and DU145).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124733/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513295
Series		Accession: GSE124733	ID: 200124733

1228. Tumor & Tumor-Adj Gene Expression in the Nurses' Health Study Cohorts
(Submitter supplied) Gene expression data from the Nurses' Health Study
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platforms: GPL22920 GPL17585 1577 Samples
FTP download: GEO (CEL, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115577/
Series		Accession: GSE115577	ID: 200115577

1229. CRISPR-based multimodal genetic screens in human iPSC-derived neurons
(Submitter supplied) CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. Most previous CRISPR-based screens were implemented in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL24676 GPL20301 14 Samples
FTP download: GEO (MTX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124703/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA513160
Series		Accession: GSE124703	ID: 200124703

1230. Aberrant enhancer reprogramming drives hepatic carcinogenesis through global transcriptional reprogramming [RNA-seq]
(Submitter supplied) ﻿Hepatocellular carcinomas (HCC) exhibit distinct promoter hypermethylation patterns, but the epigenetic regulation and function of transcriptional enhancers remain unclear. Here, our affinity- and bisulfite-based whole-genome sequencing analyses reveal global enhancer hypomethylation in human HCCs. Integrative epigenomic characterization further pinpoints a recurrent hypomethylated enhancer of CCAAT/enhancer-binding protein-beta (C/EBPβ) which correlates with C/EBPβ over-expression and poorer prognosis of patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123098/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507539
Series		Accession: GSE123098	ID: 200123098

1231. RNA sequencing results of L1-FGGY+/- lung squamous cell carcinoma tumor samples
(Submitter supplied) In order to explore pathways which were affected by L1-FGGY in lung squamous cell carcinoma (LUSC), we performed RNA sequencing on L1-FGGY+/- LUSC tumor samples. We identified 1529 (826 up and 703 down) dysregulated genes in L1-FGGY positive tissues with an adjusted p value less than 0.05. The KEGG enrichment analysis indicated that many signaling pathways were upregulated in L1-FGGY positive tissues, including glutathione metabolism, metabolism of xenobiotics by cytochrome P450, arachidonic acid metabolism, metabolic pathways, and glycerolipid metabolism, most of which were metabolic pathways, especially in lipid-related metabolism.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124625/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512867
Series		Accession: GSE124625	ID: 200124625

1232. Development of a selective CDK7 covalent inhibitor reveals predominant cell cycle phenotype
(Submitter supplied) The relationship between promoter proximal transcription factor-associated gene expression and super-enhancer-driven transcriptional programs are not well-defined. Some level of their distinct genomic occupancy may suggest a mechanism with specific target gene control. We explored the transcriptional and functional interrelationship between E2F transcription factors and BET transcriptional co-activators in multiple myeloma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124607/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512643
Series		Accession: GSE124607	ID: 200124607

1233. Induction and Therapeutic Targeting of Human NPM1c+ Myeloid Leukemia in the Presence of Autologous Immune System in Mice
(Submitter supplied) Purpose: To understand the molecular mechanisms underlying NPM1c-mediated tumorigenesis by comparing the transcriptome of de novo generated bulk human leukemic cells and leukemic stem cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512457
Series		Accession: GSE124538	ID: 200124538

1234. The Jumonji-domain histone demethylase inhibitor JIB-04 deregulates oncogenic programs and increases DNA damage in Ewing Sarcoma, resulting in impaired cell proliferation and survival, and reduced tumor growth
(Submitter supplied) The overall goal of this study was to characterize the activity and mechanism(s) of action of the pan-Jumonji domain histone demethylase small molecule inhibitor JIB-04 in the pediatric bone and soft tissue cancer Ewing Sarcoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119832/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490386
Series		Accession: GSE119832	ID: 200119832

1235. Transcriptome Analysis of Huh7 cells Infected with Adenovirus Overexpression GSTZ1 or PCK1
(Submitter supplied) Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117822/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483237
Series		Accession: GSE117822	ID: 200117822

1236. MicroRNA (miR)-211 loss promotes metabolic vulnerability and BRAF inhibitor sensitivity in melanoma
(Submitter supplied) We report that miR-211 loss-of-function in the pigmented melanoma cell line SKMEL-28  slowed growth and invasion in vitro, inhibited phosphoinositol-3-kinase (PI3K) signaling,  rendered these melanoma cells metabolically vulnerable by attenuating mitochondrial respiration and tricarboxylic acid (TCA) cycling and inhibited melanoma growth in vivo.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109378/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430713
Series		Accession: GSE109378	ID: 200109378

1237. Proteolytic cleavage by taspase1 and the regulation of the stability of MLL1
(Submitter supplied) Chromosomal translocations of the Mixed-lineage leukemia 1 (MLL1) gene generate MLL-chimeras that drive pathogenesis of acute myeloid and lymphoid leukemia.  The untranslocated MLL1 is a substrate for proteolytic cleavage by the endopeptidase, taspase1, however, the biological significance of MLL1 cleavage by this endopeptidase remains unclear. Here, we demonstrate that taspase1-dependent cleavage of MLL1 results in the destabilization of full-length MLL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 68 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355862
Series		Accession: GSE90762	ID: 200090762

1238. Fbxo32 mediated gene expression program underlies EMT and metastasis
(Submitter supplied) The epithelial-mesenchymal transition (EMT) is a process by which cells lose their cell contacts and gain migratory and invasive properties. EMT is essential for numerous developmental processes including neural tube formation, in wound healing, organ fibrosis and cancer metastasis. Despite progress, the repertoire of factors involved in global transcriptional reprogramming underlying EMT remains unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77408/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA310235
Series		Accession: GSE77408	ID: 200077408

1239. lncRNA-PCAT1 knockdown effect on the gene expression of androgen independent LNCaP (LNCaP-AI) cell line
(Submitter supplied) We generated and characterized an androgen-independent LNCaP-AI cell line by long-term culture of androgen-dependent LNCaP cells in RPMI-1640 medium containing charcoal-stripped serum. This approach used to generate the line mimics the castration resistant condition for treating prostate cancer, supporting the relevance of the LNCAP-AI cell line to Castration Resistant Prostate Cancer. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512282
Series		Accession: GSE124519	ID: 200124519

1240. LARP7 is a substrate of BRCA1 that regulats genome instability and tumorigenesis
(Submitter supplied) Impaired DNA repair leads to cancer, aging and many genetic diseases. However, understanding of the complexity of DNA is far from complete, resulting in the failure of therapies using genotoxic reagents. Here, we found that LARP7, an RNA-binding protein known to stabilize 7SK RNA, was degraded after DNA injury caused by ionizing radiation and chemotherapy. The LARP7 degradation was catalyzed by an E3 ligase complex of BRCA1 and BARD1 that was triggered by ATM-mediated phosphorylation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124393/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511893
Series		Accession: GSE124393	ID: 200124393

1241. Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration
(Submitter supplied) Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nuclear TDP-43. Here we identify that TDP-43 regulates expression of the neuronal growth-associated factor stathmin-2. Lowered TDP-43 levels, which reduce its binding to sites within the first intron of stathmin-2 pre-mRNA, uncover a cryptic polyadenylation site whose utilization produces a truncated, non-functional mRNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122069/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503396
Series		Accession: GSE122069	ID: 200122069

1242. The SUMO Pathway as a Therapeutic Option in Pancreatic Cancer
(Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) still carries a dismal prognosis with overall five-year survival of 8%. Conventional combination chemotherapies are a clear advance in the treatment of PDAC, however subtypes of the disease exist, which exhibit extensive resistance to such therapies. Genomic MYC amplifications represent a distinct subset of PDAC with an aggressive tumor biology. It is clear that hyperactivation of MYC generates dependencies, which can be exploited therapeutically. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119423/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489233
Series		Accession: GSE119423	ID: 200119423

1243. RNA-seq for prostate cancer cell lines under oxidative stress with or without PAGE4 overexpression
(Submitter supplied) RNA-seq for prostate cancer cell lines DU145 and 22RV1 with or without PAGE4 overexpression with hydrogen peroxide or PBS treatment
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487724
Series		Accession: GSE119005	ID: 200119005

1244. Expression alterations induced by restoration of AXIN1 expression in SNU449 hepatocellular carcinoma cells
(Submitter supplied) Aberrant activation of Wnt/β-catenin signaling is observed in numerous cancers. In hepatocellular carcinoma activating mutations in CTNNB1 (20-25%) or loss of function mutations in AXIN1 (10%), AXIN2 (2%) and APC (1-2%) are observed. All these mutations lead to aberrant stabilization of β-catenin, which constitutively activates downstream Wnt/β-catenin target genes and triggers a genetic program resulting in tumor formation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487644
Series		Accession: GSE119001	ID: 200119001

1245. Gene expression changes in THP1 cells at day 2 and 4 following shRNA knock-down of RUVBL2
(Submitter supplied) We used an inducible shRNA system and RNA-Seq to examine gene expression changes in acute myeloid leukemia THP1 cells following silencing of RUVBL2. RUVBL2 is a AAA+ ATPase that functions in a number of cellular processes, including chromatin remodeling and transcriptional control, and is critical for survival of acute myeloid leukemia cells and in vivo disease progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481053
Series		Accession: GSE117106	ID: 200117106

1246. The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on IMR90 transcriptome
(Submitter supplied) Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) and partially fragmented NSF-HA (fNSF-HA) on the transcriptome of IMR90 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116759/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480072
Series		Accession: GSE116759	ID: 200116759

1247. ChIP-seq and RNA-seq from human lymphoma cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114270/
Series		Accession: GSE114270	ID: 200114270

1248. RNA-seq data from human lymphoma cell lines
(Submitter supplied) RNA-seq experiments were performed on OCI-Ly19 EZH2-wild type cell line (LY19WT) and a syngenic OCI-Ly19 cell line expressing the mutated protein EZH2-Y646F (LY19Y646F). We investigated the transcriptome changes between the two conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114265/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA470706
Series		Accession: GSE114265	ID: 200114265

1249. Leucegene: AML sequencing (part 6)
(Submitter supplied) RNA-sequencing of human acute promyelocytic leukemias
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106272/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416098
Series		Accession: GSE106272	ID: 200106272

1250. Reversible LSD1 Inhibition with HCI-2509 induces the p53 gene expression signature in high-risk neuroblastoma cells
(Submitter supplied) Lysine-Specific Demethylase 1 (LSD1) over-expression correlates with poorly differentiated neuroblastoma and predicts poor outcome despite multimodal therapy. We have studied the efficacy of reversible and specific LSD1 inhibition with HCI-2509 in neuroblastoma cell lines and particularly the effect of HCI-2509 on the transcriptomic profile in MYCN amplified NGP cells.  Cell survival assays show that HCI-2509 is cytotoxic to poorly differentiated neuroblastoma cell lines in low micromole or lower doses. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412925
Series		Accession: GSE104526	ID: 200104526

1251. Transcriptomic analysis of Multiple Myeloma bone marrow microenvironment
(Submitter supplied) We report the RNA sequencing of the non-tumoral CD138- fractions of 74 MM patient BM aspirates taken at the time of diagnosis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 74 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104171/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA411890
Series		Accession: GSE104171	ID: 200104171

1252. Transcriptomic analysis to underly the heterogeneity between 4 cellular models derived from patients diagnosed with pediatric high-grade gliomas under controlled atmosphere (modulation of oxygen level).
(Submitter supplied) Generation of preclinical models which recapitulate at best the extreme intra-tumoral heterogeneity (using two cell culture conditions) and inter-tumor heterogeneity between children diagnosed with high-grade gliomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101799/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395554
Series		Accession: GSE101799	ID: 200101799

1253. Flura-Seq Identifies In Situ Transcriptomes of Micrometastases
(Submitter supplied) Understanding the biology of rare cell populations in the context of their microenvironment requires an accurate analysis of the transcriptomes of these cells as expressed in situ. We developed fluorouracil-tagged RNA sequencing (Flura-seq) to characterize the transcriptomes of small cell subpopulations from a whole organ in model systems. The method utilizes cytosine deaminase (CD), which converts the non-natural pyrimidine base fluorocytosine to fluorouracil. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16512 GPL11154 30 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93605/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361272
Series		Accession: GSE93605	ID: 200093605

1254. Wiskott-Aldrich Syndrome-causative mutations disrupt alternative splicing and promote gene networks predisposed to hematologic malignancies
(Submitter supplied) Wiskott-Aldrich syndrome (WAS) is characterized by X-linked thrombocytopenia, eczema, immunodeficiency, recurrent infections and increased risk of autoimmunity and malignancies. WAS is caused by mutations in the WAS gene, which encodes the exclusively hematopoietic WAS protein (WASp) that is classically characterized as aν actin nucleator. However, disruption of F-actin polymerization by WAS mutations can not account for many aspects of WAS pathogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77129/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309524
Series		Accession: GSE77129	ID: 200077129

1255. An atlas of genetic influences on osteoporosis in humans and mice
(Submitter supplied) In our study, we leveraged RNA-seq data from four different human osteoblast cell lines and ATAC-seq data from one human osteoblast cell line to identify target genes for plausibly causal SNPs influencing bone density. We also re-called ENCODE generated osteoblast DNase hypersensitive sites, and have uploaded them here for sharing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120755/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494401
Series		Accession: GSE120755	ID: 200120755

1256. Immune determinants for the mesenchymal identity of ovarian cancer via exosome-mediated microRNA transfer
(Submitter supplied) Ovarian cancer is a heterogeneous disease that constitutes great menace to female health and poses tremendous clinical challenge. Based on unsupervised classification of whole-genome gene expression profiles, four molecular subtypes of ovarian cancer were recently identified. However, currently it is still unelucidated on the immune infiltration pattern of different molecular subtypes of ovarian cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120354/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492873
Series		Accession: GSE120354	ID: 200120354

1257. Inhibition of the integrin alpha-V beta-3 reverts the paradoxical effect of levothyroxine replacement during bexarotene therapy in cutaneous T-cell lymphoma
(Submitter supplied) Bexarotene is a specific RXR agonist that has been used for the treatment of cutaneous T-cell lymphoma (CTCL). The mechanism of action is pleiotropic but impacts directly on CTCL cell proliferation, chemotaxis and apoptosis, and indirectly on lymphoma immunity. Bexarotene causes hypothyroidism in more than 90% of patients thus requiring the concomitant administration of levothyroxine. Hereon we investigated the consequence of levothyroxine administration to the antineoplastic effect of bexarotene in CTCL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119345/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488816
Series		Accession: GSE119345	ID: 200119345

1258. Profiling and bioinformatics analyses reveal differential expression of circular RNA in tongue cancer revealed by high-throughput sequencing
(Submitter supplied) Circular RNAs (circRNA) are special non-coding RNAs. They are widely present, but with unknown functions. Recent studies have shown that many endogenous circRNAs have sponge function to absorb microRNAs. They can regulate target gene mRNA expression and play important roles in many biological processes. However, expression profile and function of circRNAs in human TSCC haven’t been reported. High-throughput sequencing was performed to identify and annotate from three TSCC tissues and adjacent tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118750/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486674
Series		Accession: GSE118750	ID: 200118750

1259. Genome-wide maps of human adenocarcinomal cell PC-9 and LINC00312 knockdown PC-9 cell
(Submitter supplied) We performed RNA-seq to analyze the transcriptional profiles of PC-9 cells with reduced expression of LINC00312 to better understand the molecular mechanisms by LINC00312
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482470
Series		Accession: GSE117564	ID: 200117564

1260. RNA deep sequencing analysis of human brain microvascular endothelial cells (ECs) treated with glioma-conditioned medium (glioma-CM)
(Submitter supplied) To determine the effects of glioma-conditioned medium on global gene expression in ECs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476304
Series		Accession: GSE115850	ID: 200115850

1261. snRNAs as regulators of alternative splicing
(Submitter supplied) In this study we investigated snRNA-mediated modulation of pre-mRNA splicing across the human transcriptome. We first quantified the relative abundance of snRNAs across a comprehensive range of healthy adult and fetal tissues, revealing a surprising variation in the relative snRNA levels both inter- and intra-tissue. To study the role of snRNAs in cancer-relevant splicing, we used breast cancer as a model, since it exhibits a high rate of aberrant splicing48, but a low frequency of mutations in the splicing machinery52. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107163/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419192
Series		Accession: GSE107163	ID: 200107163

1262. Transcriptome analysis on TDP43 and SRSF3 downstream genes and binding RNAs in MDA-MB231 cells by Next Generation Sequencing
(Submitter supplied) TDP43 and SRSF3 has been reported to be RNA-binding proteins; however their roles in breast cancer progression has not been  examined previously. Here, we performed RNA-seq on MDA-MB231 cells stably expressed sh-control, shTDP43, shSRSF3 or sh-TDP43 and sh-SRSF3 using lentivirus in duplicates. In addition, MDA-MB231 cells with stable expression of flag-TDP43 or flag-SRSF3 were also generated by using lentivirus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383668
Series		Accession: GSE98016	ID: 200098016

1263. Methylome, hydroxymethylome, and integrative transcriptome profiling in human CRC tissue and paired normal tissues
(Submitter supplied) DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks in the carcinogenesis of colorectal cancer by transcriptional regulation. 5hmC is an intermediate during active demethylation and maintains the equilibrium of DNA methylation. Previous studies on DNA methylation don’t differentiate 5-hmC from 5-mC. Here, in order to elucidate the epigenetic mechanisms of carcinogenesis of colorectal cancer, we integrate genome wide levels of 5-mC, 5-hmC and Transcriptional expression. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT, WIG, XML) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87096/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343496
Series		Accession: GSE87096	ID: 200087096

1264. Whole blood RNA sequencing in idiopathic pneumonia syndrome reveals a unique transcriptomic profile compared to ARDS
(Submitter supplied) The acute respiratory distress syndrome (ARDS) is a highly lethal syndrome characterized by hypoxemia and bilateral lung infiltrates in response to an inciting event such as sepsis. Allogeneic bone marrow transplantation (BMT) is a life-saving treatment for patients with hematologic malignancies that can be complicated by ARDS. We sought to identify blood gene expression signatures that distinguish whether ARDS in BMT may be a distinct pathobiologic entity from ARDS in non-BMT patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 26 Samples
FTP download: GEO (CSV, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84439/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329148
Series		Accession: GSE84439	ID: 200084439

1265. FTO Regulates Activation of Rho GTPases Signaling as N6-methyladenosine RNA Demethylase and an Rhotekin Partner Protein
(Submitter supplied) Reversible RNA modification of N6-methyladenosine (m6A) plays a critical role in post-transcriptional gene regulation1-13. Although the fat mass and obesity-associated protein (FTO) has been previously shown to function as an m6A demethylase in nuclear RNA1,14, its exact function in disease pathogenesis remains a mystery. Here, we demonstrate that FTO suppresses the activation of Rho GTPase signaling via both its demethylation activity and specific interaction with Rho effector, Rhotekin (RTKN)15. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83540/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326275
Series		Accession: GSE83540	ID: 200083540

1266. RNA-seq profiles after SP-2509 Treatment of LNCaP, C42B, and PC3 cells
(Submitter supplied) LSD1 (also known as KDM1A) is a histone demethylase and a key regulator of gene expression in embryonic stem cells and cancer.1,2 LSD1 was initially identified as a transcriptional repressor via its demethylation of active histone H3 marks (di-methyl lysine 4 [2MK4]).1  In prostate cancer, specifically, LSD1 also co-localizes with the AR and demethylates repressive 2MK9 histone marks from androgen-responsive AR target genes, facilitating androgen-mediated induction of AR-regulated gene expression and androgen-induced proliferation in androgen-dependent cancers.3,4  Recently, it was shown that treatment with high doses of androgens (e.g.10-fold higher doses than those required for induction of expression of androgen-activated genes such as PSA) recruits LSD1 and AR to an enhancer within the AR; this AR and LSD1 recruitment represses AR transcription.5 Thus, LSD1 appears to play a role in mediating both the proliferative and repressive phases of the biphasic androgen dose-response curve. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59009/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA254103
Series		Accession: GSE59009	ID: 200059009

1267. Parental and Vemurafenib-resistant UACC62 melanoma cells
(Submitter supplied) Over half of cutaneous melanoma tumors have BRAFV600E/K mutations. Acquired resistance to BRAF inhibitors (BRAFi) remains a major hurdle in attaining durable therapeutic responses. In this study we demonstrate that approximately 50-60% of melanoma cell lines with acquired Vemurafenib resistance activate the RhoA family signaling pathway. RhoAHigh BRAFi-resistant cells are sensitive to the combination of ROCK inhibitors and Vemurafenib. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115938/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476556
Series		Accession: GSE115938	ID: 200115938

1268. Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes (PHOX2B)
(Submitter supplied) Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512028
Series		Accession: GSE124451	ID: 200124451

1269. Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes (ALK)
(Submitter supplied) Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124450/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512029
Series		Accession: GSE124450	ID: 200124450

1270. A runaway PRH/HHEX-Notch3 feedback loop drives cholangiocarcinoma (RNA-Seq)
(Submitter supplied) PRH/HHEX-Notch3 feedback loop drives cholangiocarcinoma
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124429/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA512000
Series		Accession: GSE124429	ID: 200124429

1271. Diminished OPA1 expression and impaired mitochondrial morphology and homeostasis in Aprataxin-deficient cells
(Submitter supplied) Ataxia with oculomotor apraxia type 1 (AOA1) is an early onset progressive spinocerebellar ataxia caused by mutation in aprataxin (APTX). Here we use RNA-seq to identify genes that are affected by APTX-KO, APTX overexpression, and APTX mutant, thus contributes to understadning the mechanisms underlying AOA1 pathlogy.  Published: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz083/5319145
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 10 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124412/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511981
Series		Accession: GSE124412	ID: 200124412

1272. Genes altered in expression by knockdown of PTK2 in breast cancer cell lines
(Submitter supplied) PTK2 was knocked down by doxycycline-dependent expression of small hairpin RNA against PTK2 in Breast cancer cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427773
Series		Accession: GSE108596	ID: 200108596

1273. CDK4/6 inhibition sensitizes myeloma to lenalidomide by reducing the MEIS2 to CRBN ratio that accelerates IKZF1 and IKZF3 degradation
(Submitter supplied) The RNA-seq data presented in this study include libraries from bone marrow plasma cells (BMPC), primary myeloma cells (BMMCs) from 7 patients, and myeloma cell line MM1.S and KMS12
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76425/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307260
Series		Accession: GSE76425	ID: 200076425

1274. Dysfunctional CD8+ T cells form a proliferative, dynamically regulated compartment within human melanoma [scRNA-seq]
(Submitter supplied) Tumor immune cell compositions play a major role in response to immunotherapy but the heterogeneity and dynamics of immune infiltrates in human cancer lesions remain poorly characterized. Here we identify conserved intratumoral CD4 and CD8 T cell behaviors in  scRNA-seq data from 25 melanoma patients. We discover a large population of CD8 T cells showing continuous progression from an early effector “transitional” into a dysfunctional T cell state. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 204 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123139/
Series		Accession: GSE123139	ID: 200123139

1275. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic  signaling in the intestine
(Submitter supplied) Aim: RNA binding proteins (RBPs) are expressed broadly during both development and malignant transformation, yet their mechanistic roles in epithelial homeostasis or as drivers of tumor initiation and progression are incompletely understood. Method: Here we describe a novel interplay between RBPsLIN28B and IMP1 in intestinal epithelial cells. Ribosome-profiling and RNA-sequencing identifies IMP1 as a principle nodefor gene expression regulation downstream of LIN28B. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115647/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475675
Series		Accession: GSE115647	ID: 200115647

1276. Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
(Submitter supplied) Sea spray aerosols (SSAs) have profound effects on our climate and ecosystems. They also contain microbiota and biogenic molecules which could affect human health. Yet the exposure and effects of SSAs on human health remain poorly studied. Here, we exposed human lung cancer cells to extracts of a natural sea spray aerosol collected at the seashore in Belgium, a laboratory-generated SSA, the marine algal toxin homoyessotoxin and a chemical inhibitor of the mammalian target of rapamycin (mTOR) pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113144/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450210
Series		Accession: GSE113144	ID: 200113144

1277. Genome-wide transcript profiling of human prostate stromal cells in response to genotoxic treatment and SASP inhibitors
(Submitter supplied) Cancer develops in a complex environment that encompasses a wide spectrum of benign cell types, while the local microenvironment reduces the efficacy of multiple forms of cancer therapies. The DNA damage secretory program (DDSP) provoked by the side effects of genotoxic therapeutics results in cellular senescence and the senescence-associated secretory phenotype (SASP), the side effects of the latter frequently fueling advanced pathologies particularly therapeutic resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by array
Platform: GPL16956 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90866/
Series		Accession: GSE90866	ID: 200090866

1278. Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118871/
Series		Accession: GSE118871	ID: 200118871

1279. Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation II
(Submitter supplied) The transcriptional profile of A673 parental,  and SP-2509 drug resistant washout cells (4 and 6 months)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118870/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487073
Series		Accession: GSE118870	ID: 200118870

1280. Ewing sarcoma resistance to SP-2509 is not mediated through KDM1A/LSD1 mutation I
(Submitter supplied) The transcriptional profile of A673 parental and SP-2509 Drug resistant cells treated with DMSO and SP-2509 (2uM 48hrs)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118864/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487071
Series		Accession: GSE118864	ID: 200118864

1281. Genome wide expression change in LCC2 and MCF-7 cells
(Submitter supplied) We aim to the investigate the role of tamoxifen in breast cancer progression. LCC2 and MCF-7 cells were used as the resistant and sensitive model.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486779
Series		Accession: GSE118774	ID: 200118774

1282. Self-associated molecular patterns mediate cancer immune evasion by engagement of Siglec receptors
(Submitter supplied) Cancer immunotherapy targeting inhibitory receptors on T cells has changed the landscape of oncological practice, but most patients do not respond to current approaches. Thus, new targets on T cells for cancer immunotherapy are needed. CD33-related Siglecs are pattern recognition immune receptors binding to a broad range of sialoglycan ligands, which appear to function as self-associated molecular patterns (SAMPs) to dampen unwanted immune responses against self. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474508
Series		Accession: GSE115305	ID: 200115305

1283. ChIPseq and RNAseq analysis of T47D cells with/without  silencing TRPS1/CHD4
(Submitter supplied) We reported the transcriptional regulation function and mechanism of TRPS1-CHD4/NuRD.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (BED, PY, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114213/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA470671
Series		Accession: GSE114213	ID: 200114213

1284. Determine the role of TXNDC9 in hepatocellular carcinoma progression
(Submitter supplied) Thioredoxin Domain Containing 9 (TXNDC9)  is a member of the thioredoxin family. The exact function of this protein is not known. This experiment is a transcriptiome profiling of  TXNDC9 dependent RNA expression in hepatocellular carcinoma cell line HepG2.  By compairing the gene expression profile of WT and TXNDC9 knockout, we identified some genes directly or indirectly regulated by TXNDC9 in hepatocellular carcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113400/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451023
Series		Accession: GSE113400	ID: 200113400

1285. A consensus hypoxia signature in breast cancer
(Submitter supplied) We exposed a panel of 32 breast cancer cell lines or normal human mammary epithelial cells to 20% or 1% O2 concentration for 24h. Total RNA was extracted from cells using TRIzol (Invitrogen) and treated with DNase I (Ambion). All samples had a RIN value of >9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 64 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111653/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437670
Series		Accession: GSE111653	ID: 200111653

1286. Heterogeneous maintenance of human tissue resident memory T cells based on efflux capacities
(Submitter supplied) Tissue-resident memory T cells (TRM) accelerate pathogen clearance through rapid and enhanced functional responses in situ. In humans, TRM cells are prevalent in diverse anatomic sites throughout the human lifespan, yet mechanisms for long-term maintenance are unknown. Here, we identify subpopulations of human TRM in mucosal and lymphoid sites based on differential efflux of mitochondrial dyes, with distinct transcriptional profiles, turnover, and functional capacities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109841/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432166
Series		Accession: GSE109841	ID: 200109841

1287. Transcriptome analysis of VCaP xenografts resistant to dual therapy with abiraterone and enzalutamide
(Submitter supplied) We report RNA sequencing data on serial biopsies of prostate cancer VCaP xenografts as the tumors pass from androgen-sensitivity (Pre-Cx), to castration resistance (CRPC, castration resistant prostate cancer), onto resistance to dual therapy with abiraterone plus enzalutamide (AER). From comparison of these RNAseq data sets, we were able to determine differentially expressed genes between the AER/CRPC and Pre-Cx states that could mediate resistance to androgen deprivation therapies.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431777
Series		Accession: GSE109708	ID: 200109708

1288. Differential expression of pancreatic cancer  PANC1 cells treated with pilocarpine
(Submitter supplied) Human Panc1 cells were treated with 1mM  Pilocarpine and the differential expression measured by RNASeq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102880/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399152
Series		Accession: GSE102880	ID: 200102880

1289. Metastasis in triple negative breast cancer is dependent on ΔNp63/CXCL2/CCL22-mediated recruitment of myeloid-derived suppressor cells
(Submitter supplied) Gene expression analysis of the knockdown of ΔNP63 in two different human breast cancer cell lines using RNA-Seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397593
Series		Accession: GSE102377	ID: 200102377

1290. Induced DNA demethylation, genome instability and transcription
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by array
Platforms: GPL23391 GPL16791 18 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98693/
Series		Accession: GSE98693	ID: 200098693

1291. Impact of DNA demethylation agents (5-azacytidine or vitamin C) on gene expression in glioblastoma HSR-GBM1 cells
(Submitter supplied) Glioblastoma HSR-GBM1 cells have low mitochondrial DNA copy numbers which is associated with the abnormal DNA methylation patterns. By inducing DNA demthylation using 5azacytidine and vitamin C, HSR-GBM1 cells modulate their mitochondrial copy number and capability of differentiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98692/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385927
Series		Accession: GSE98692	ID: 200098692

1292. RNA-sequencing of milk cells extracted from pre-partum secretions and longitudinally from mature human milk across the first year of lactation
(Submitter supplied) Changes in mammary cell behavior mediating normal breast development during pregnancy and lactation are poorly understood due to limited availability of breast biopsies during this time. Human milk contains a hierarchy of cells including stem cells, mature milk producing cells (lactocytes) and myoepithelial cells. Here we non-invasively sampled the total epithelial cell population of the lactating mammary gland from mature HM collected from healthy mother/infant dyads during the first year postpartum, and explored temporal changes in the mammary cell transcriptome using RNA sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85494/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338656
Series		Accession: GSE85494	ID: 200085494

1293. Identification of novel recurrent ETV6-IGH fusions in primary central nervous system lymphoma using high throughput RNA sequencing
(Submitter supplied) We provide a novel gene fusion (ETV6-IgH) involving a truncation of ETV6 and leading to haploinsuffiency of ETV6 expression. ETV6-IgH is a new potential surrogate marker of PCNSL with favorable prognosis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322631
Series		Accession: GSE81816	ID: 200081816

1294. RNA Methyltransferase METTL14 Promotes Breast Cancer Growth and Progression
(Submitter supplied) We investigated the role of RNA N6-adenosine methyltransferase protein METTL14 that supports breast cancer growth and progression, and we showed METTL14 knockdown inhibited long-term survival, migration as well as invasion of breast cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81164/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320762
Series		Accession: GSE81164	ID: 200081164

1295. UBC9 knockdown  in bladder cancer T24 cell lines
(Submitter supplied) UBC9 is the sole conjugating enzyme E2 in the sumoylation and plays a pivotal role in maintaining homeostasis and restraining stress reaction. Targeting UBC9 is emerging as a novel strategy for cancer therapy. However, the role of UBC9 in bladder cancer is not clear. Here, we sought to determine the alterations of trancriptome after shRNA-mediated knockdown UBC9 in T24 cell lines．
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117143/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481271
Series		Accession: GSE117143	ID: 200117143

1296. Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 19 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114070/
Series		Accession: GSE114070	ID: 200114070

1297. Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer [RNA-Seq]
(Submitter supplied) Metastatic medullary thyroid cancer (MTC) is a currently incurable disease. FDA approved therapies that target RET, a commonly mutated receptor tyrosine kinase in MTC, and other receptor tyrosine kinases, do not result in complete responses and acquired resistance is universal due to “gatekeeper” mutation in Ret or overactivation of alternative signaling pathways. Based on data from human MTCs and a number of murine models, the CDK/RB cell cycle pathway is a potential alternative target for MTC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114069/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464055
Series		Accession: GSE114069	ID: 200114069

1298. Immortalized breast epithelial cell lines from normal breast with luminal and intrinsic subtypes – enriched gene expression
(Submitter supplied) The cell-type origin has long been suspected to determine molecular features of tumors but has proven difficult to experimentally validate in human breast cancers because of deficiencies in culturing methods that allow propagation of three major cell types of the breast including stem/basal, luminal-progenitor and mature/differentiated cells. We have created immortalized cell lines from core breast biopsies of ancestry-mapped healthy women that are enriched for luminal gene expression including hormonally sensitive ERa-FOXA1-GATA3 transcription factor network. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 59 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427584
Series		Accession: GSE108541	ID: 200108541

1299. Mechanisms of Cancer Resistance to Immunogenic Cytotoxicity
(Submitter supplied) The majority of cancer patients do not respond to immunotherapy. In order to systematically discover pathways promoting cancer cell resistance to effector immune cells, we generated immunity-resistant Head and Neck Squamous Cell Carcinoma cell lines. We utilized RNA-Seq to determine what are the genes and pathways that are significantly altered when cancer cells become resistant to effectors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100828/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393191
Series		Accession: GSE100828	ID: 200100828

1300. RNA-Seq analysis of human colorectal cancer with liver metastasis
(Submitter supplied) Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92914/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358825
Series		Accession: GSE92914	ID: 200092914

1301. Pre-invasive versus microinvasive carcinoma of the cervix
(Submitter supplied) Comparative analysis of gene expression prodfiles of cervical biopsy from two (2) patients with pre-invasive neoplastic lesions (carcinonma in citu, or high-grade cervical intraepithelial neoplasia) and 2 patients with earliest stage of invasive cancer
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124288/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511468
Series		Accession: GSE124288	ID: 200124288

1302. Polycomb Group Proteins EZH2 and EED Directly Regulate Androgen Receptor in Advanced Prostate Cancer
(Submitter supplied) Polycomb group proteins are important epigenetic regulators for organ development, cell proliferation and differentiation, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including EZH2, promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells. The canonical function of EZH2, along with its essential binding partners EED and SUZ12, is to methylate histone H3K27 and repress its downstream targets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124268/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA511443
Series		Accession: GSE124268	ID: 200124268

1303. Rescue of premature aging defects in Cockayne Syndrome Derived Stem Cells by Targeted Gene Correction
(Submitter supplied) Cockayne Syndrome (CS) is a rare autosomal recessive inherited disorder characterized by a variety of clinical features including sensitivity to sunlight, progressive neurological abnormalities and appearance of premature aging. However, the pathogenesis of CS yet remains unclear due to the limitations of current disease models. Here we generate integration free-induced pluripotent stem cells (iPSCs) from CS patient fibroblast bearing mutations in CSB/ERCC6 and further derive isogenic gene corrected (GC)-iPSCs using CRISPR/Cas9 system. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124208/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510990
Series		Accession: GSE124208	ID: 200124208

1304. Wnt1 silences CC/CXC motif chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma
(Submitter supplied) Lung adenocarcinoma (LUAD)-derived oncogenic Wnts increase cancer cell proliferative/stemness potential, but whether they also impact the immune microenvironment is unknown. Here we show that LUAD cells use paracrine Wnt1 signaling to induce immune resistance. Wnt1 correlated strongly with tolerogenic genes on the TCGA expression data. In another cohort, Wnt1 was inversely associated with T cell abundance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510981
Series		Accession: GSE124199	ID: 200124199

1305. PLZF limits enhancer activity during hematopoietic progenitor aging
(Submitter supplied) PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment. PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors but little is known about its role in remodeling chromatin of cells committed towards a given specific hematopoietic lineage. In murine myeloid progenitors, we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac). more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 GPL18480 41 Samples
FTP download: GEO (BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE124nnn/GSE124190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510975
Series		Accession: GSE124190	ID: 200124190

1306. Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types.
(Submitter supplied) We reported transcriptional characterization of tumor-infiltrating T regulatory cells (TITRs) that is shared between species and among different tumor types and stages. We genomically profiled immunocytes from 2 species: 1. Mouse: CD4+ Treg and Tconv, and CD8+ T cells from tumor and spleen of B16, MC38 or CT26 tumor bearing mice, as well as from spleens of non-tumor bearing mice. 2. Human: CD4+ Treg cells from surgically resected and cryopreserved human colorectal carcinomas or normal colon tissue.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 78 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116347/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478226
Series		Accession: GSE116347	ID: 200116347

1307. Single cell RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from
(Submitter supplied) Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107794/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421423
Series		Accession: GSE107794	ID: 200107794

1308. Bulk RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from
(Submitter supplied) Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107793/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421424
Series		Accession: GSE107793	ID: 200107793

1309. Deconstructing Retinal Organoids: single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina
(Submitter supplied) The rapid improvements in single cell sequencing technologies and analyses methods afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-Sequencing at three time points of differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 79 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119893/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490648
Series		Accession: GSE119893	ID: 200119893

1310. RNA expression in BRCA2-depleted breast cancer cell lines
(Submitter supplied) Next generation RNA sequencing was performed to analyze changes in gene expression upon BRCA2 depletion. BRCA2 depletion was introduced in two human breast cancer cell lines with doxycyclin inducible short hairpin RNAs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116943/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480663
Series		Accession: GSE116943	ID: 200116943

1311. Molecular variability of patient-derived colon tumor xenografts
(Submitter supplied) Primary tumors and their corresponding P2 mouse xenografts were surveyed for gene expression using the RNA-sequencing approach.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 57 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112941/
Series		Accession: GSE112941	ID: 200112941

1312. Colorectal Adenomas and Consensus Molecular Subtyping
(Submitter supplied) Consensus molecular subtyping in adenomatous and serrated polyps
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108317/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423096
Series		Accession: GSE108317	ID: 200108317

1313. SOX11 knockdown in B-ALL cell lines
(Submitter supplied) Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal and proliferative features. We sought to identify transcription factors that exhibit altered and subtype-specific expression pattern in B-ALL, and report here that SOX11, a developmental and neuronal TF is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123943/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA510364
Series		Accession: GSE123943	ID: 200123943

1314. Calibrated CAR activation potential directs alternative T cell fates and therapeutic potency
(Submitter supplied) CD19-specific CARs that comprise CD28 and CD3z signaling domains program highly performing effector functions that mediate potent tumor elimination, but they impart a relatively limited T cell lifespan. Increasing functional T cell persistence without reducing effector potency is therefore likely to further enhance the therapeutic success of 1928z CAR T cells. We demonstrate that the number and position of ITAMs in 1928z CAR T cells influence functional, phenotypic and transcriptional programs, resulting in profound effects on antitumor efficacy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121226/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496405
Series		Accession: GSE121226	ID: 200121226

1315. Next Generation Sequencing for Genome-wide Maps of DNA Methylation, ChIP-seq and RNA-seq in Liver Cells
(Submitter supplied) Aberrant DNA methylation is a distinguished feature of cancer. We introduce a novel method of Guide Positioning Sequencing (GPS) for precisely detecting whole genome DNA methylation and applied GPS as well as ChIP-seq and RNA-seq in normal liver cells and hepatoma cell lines to find how abberant DNA-methylation affect gene expression and cell identity during tumorigenesis and metastasis. We systematically found that the methylation difference between genebody and promoter is an effective predictor for gene expression with a correlation coefficient of 0.7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357266
Series		Accession: GSE92328	ID: 200092328

1316. RNA-seq analysis for resistance to PI3K inhibition in Glioblastoma (GBM)
(Submitter supplied) The goal of this study is to identify the pathway alterations driving the adaptive resistance to PI3K inhibition in GBM. We generated the resistant cell lines through a patient-derived in vivo glioma sphere-forming cell (GSC) model.  We performed RNA-seq on the paired GSC samples including the parental and resistant groups. Libraries were sequenced with an average coverage for each tumor of 50x on the Hiseq4000 platform from Illumina, using 76 nt pair-ended reads. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (GCT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123821/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509924
Series		Accession: GSE123821	ID: 200123821

1317. RNA-seq data for non-targeting siRNA and lncRNA LOL siRNA transfection in MCF-7 cells
(Submitter supplied) To  elucidate which portions of signaling pathways LOL influences in luminal breast cancer, RNA-seq analysis was performed in siLOL MCF-7 cell lines. Eight hundred eighty-three downregulated genes and 1182 upregulated genes (fold change ≥1.5) were detected after LOL knockdown. Gene set enrichment analysis (GSEA) of hallmarks indicated that the gene sets related to DNA_Repair, G2M_Checkpoint, E2F_Targets and MYC_Targets were positively correlated with LOL downregulation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123820/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509922
Series		Accession: GSE123820	ID: 200123820

1318. Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes
(Submitter supplied) T-box (TBX) transcription factors are evolutionary conserved genes and master transcriptional regulators. In mammals, TBX2 subfamily (TBX2, TBX3, TBX4, and TBX5) genes are expressed in the developing lung bud and tracheae. Our group previously showed that the expression of TBX2 subfamily was significantly high in human normal lungs, but markedly suppressed in lung adenocarcinoma (LUAD). To further elucidate their role in LUAD pathogenesis, we first confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123769/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509770
Series		Accession: GSE123769	ID: 200123769

1319. Quantitative mass spectrometry-based proteomics reveals the dynamic protein landscape during initiation of human Th17 cell polarization
(Submitter supplied) CD4+ T cells play a key role in the adaptive immune system. Their subset, Th17 cells contribute to pathogenesis of inflammatory and autoimmune diseases and cancer. To reveal the Th17 cell-specific proteomic signature regulating Th17 cell differentiation and function in human we used a label-free mass spectrometry-based approach. To determine the degree of similarities and differences between the transcript and the protein levels, we performed a comprehensive analysis of the transcript-protein relationships. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 10 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118974/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487597
Series		Accession: GSE118974	ID: 200118974

1320. circ-ZNF609 regulates G1-S progression in Rhabdomyosarcoma
(Submitter supplied) Circular RNAs (circRNAs) represent a class of covalently closed RNAs, derived from a non-canonical splicing event, ubiquitously expressed among Eukaryotes and conserved among different species. We identified a circRNA (circ-ZNF609) involved in the regulation of human primary myoblast proliferation. Upon its depletion, the percentage of proliferating myoblasts was highly reduced. To deepen our knowledge about circ-ZNF609 role in cell cycle regulation, we studied its expression and function in Rhabdomyosarcoma (RMS), a pediatric skeletal muscle malignancy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117609/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482643
Series		Accession: GSE117609	ID: 200117609

1321. Local Genomic Features Predict the Distinct and Overlapping Binding Patterns of the bHLH‐Zip Family Oncoproteins MITF and MYC‐MAX
(Submitter supplied) MITF and MYC are well‐known oncoproteins and members of the basic helix‐loop‐helix leucine zipper (bHLH‐Zip) family of transcription factors (TFs) recognizing hexamer E‐box motifs. MITF and MYC not only share the core binding motif, but are also the two most highly expressed bHLH‐Zip transcription factors in melanocytes, raising the possibility that they may compete for the same binding sites in select oncogenic targets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 10 Samples
FTP download: GEO (BROADPEAK, DIFF, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115845/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476295
Series		Accession: GSE115845	ID: 200115845

1322. Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis
(Submitter supplied) The AML1-ETO fusion protein, generated by the t(8;21) chromosomal translocation, is causally involved in nearly 20% of acute myeloid leukemia (AML) cases. In leukemic cells, AML1-ETO resides in and functions through a stable protein complex, AETFC, that contains multiple transcription (co)factors. Among these AETFC components, HEB and E2A, two members of the ubiquitously expressed E proteins, directly interact with AML1-ETO, confer new DNA-binding capacity to AETFC, and are essential for leukemogenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472043
Series		Accession: GSE114644	ID: 200114644

1323. Mesothelioma xenografts in nude mice: PBS treated versus pirfenidone treated
(Submitter supplied) Background: Malignant mesothelioma is an aggressive cancer with poor prognosis. It is characterized by prominent extracellular matrix, mesenchymal tumor cell phenotypes and chemoresistance. In this study, the ability of pirfenidone to alter mesothelioma cell proliferation and migration as well as mesothelioma tumor microenvironment was evaluated. Pirfenidone is an anti-fibrotic drug used in the treatment of idiopathic pulmonary fibrosis and has also anti-proliferative activities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113803/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454010
Series		Accession: GSE113803	ID: 200113803

1324. Expression analysis of λH1-hESC derived β-like cells
(Submitter supplied) Purpose: Pancreatic islet transplantation is an effective cell therapy for type 1 diabetes (T1D), but its clinical application is limited by the shortage of donor pancreata. Among the potential alternatives, the differentiation of human embryonic stem cells (hESc) into insulin-producing β-cells has taken an early lead. However, while the proportion of β-cells obtained through current methods is relatively high, a significant percentage of undefined non-endocrine cell types are still generated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422365
Series		Accession: GSE108056	ID: 200108056

1325. Exploring the landscape of transcriptome 3’ end diversity (TREND) by applying TRENDseq
(Submitter supplied) Purpose: To identify key drivers of transcriptome 3’end diversity (TREND) in neuroblastoma in a genome wide scale. To develop and apply TRENDseq – a tailored method for genome-wide interrogation of the TREND landscape in highly multiplexed libraries.  Methods: RNA from BE(2)-C cells transfected with control or specific siRNA’s against indicated TREND regulator were processed according to TRENDseq protocol and sequenced using Illumina HiSeq 2500 or NextSeq 500. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL16791 218 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95057/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375866
Series		Accession: GSE95057	ID: 200095057

1326. An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells
(Submitter supplied) An aberrant androgen receptor (AR) transcriptional network underpins prostate cancer development. Even though the AR cistrome had been extensively studied in prostate cancers, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited due to the absence of an AR-associated chromatin interactome map. To resolve this, we utilized chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to profile AR-associated and ERG-associated long range chromatin interactions in an ERG fusion positive prostate cancer cell line. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL9115 GPL9138 GPL11154 8 Samples
FTP download: GEO (BED, BEDGRAPH, TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE54nnn/GSE54946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238129
Series		Accession: GSE54946	ID: 200054946

1327. Ultracentifugation and nanoscale deterministic lateral displacement (nanoDLD) of samples for exRNA analysis
(Submitter supplied) An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on those samples obtained via ultracentrifugation and nanoscale deterministic lateral displacement (nanoDLD).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123736/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509666
Series		Accession: GSE123736	ID: 200123736

1328. Thymine DNA Glycosylase as a novel target for melanoma: effect of TDG silencing on gene expression in SK-mel-28 melanoma cells
(Submitter supplied) Melanoma is an aggressive neoplasm with increasing incidence that is classified by the NCI as a recalcitrant cancer, i.e., a cancer with poor prognosis, lacking progress in diagnosis and treatment. In addition to conventional therapy, melanoma treatment is currently based on targeting the BRAF/MEK/ERK signaling pathway and immune checkpoints. As drug resistance remains a major obstacle to treatment success, advanced therapeutic approaches based on novel targets are still urgently needed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123681/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509566
Series		Accession: GSE123681	ID: 200123681

1329. Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 50 Samples
FTP download: GEO (BED, BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120331/
Series		Accession: GSE120331	ID: 200120331

1330. Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [RNA-Seq]
(Submitter supplied) Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 12 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120330/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492497
Series		Accession: GSE120330	ID: 200120330

1331. Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq]
(Submitter supplied) Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL15520 27 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120329/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492490
Series		Accession: GSE120329	ID: 200120329

1332. Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]
(Submitter supplied) Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (BEDGRAPH, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492493
Series		Accession: GSE120328	ID: 200120328

1333. Organoid modeling of the tumor immune microenvironment
(Submitter supplied) The interaction of neoplastic cells with their tumor microenvironment (TME) is required for cancer progression. However, in vitro cancer models, including recent in vitro 3-dimensional (3D) organoid cultures of primary human tumors, are typically comprised exclusively of neoplastic epithelium, with stromal and/or immune interactions requiring artificial reconstitution. As relevant to cancer immunotherapy, the unified co-culture of primary tumor epithelia with their endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has remained particularly elusive. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL24676 GPL20301 35 Samples
FTP download: GEO (CSV, MTX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111360/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436710
Series		Accession: GSE111360	ID: 200111360

1334. Genome-wide stability of DNA replication program in single mammalian cells
(Submitter supplied) We report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. more...
Organism:	Homo sapiens; Mus musculus
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL18460 GPL18480 GPL17303 266 Samples
FTP download: GEO (BEDGRAPH, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108556/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427668
Series		Accession: GSE108556	ID: 200108556

1335. Transcriptional changes and H3K27ac occupancy associated with resistance to JQ1 treatment in MYCN-amplified neuroblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 58 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107708/
Series		Accession: GSE107708	ID: 200107708

1336. Transcriptional changes associated with resistance to JQ1 treatment in MYCN-amplified neuroblastoma
(Submitter supplied) Drug resistance is a major clinical challenge in achieving durable responses to targeted cancer therapeutics.  Resistance mechanisms to new classes of epigenetic-targeted drugs entering the clinic remain largely unexplored.  We used BET inhibition in MYCN-amplified neuroblastoma as a prototype to model innate and acquired resistance to chromatin remodeling inhibitors in cancer. Genome-scale, pooled lentiviral ORF and CRISPR knockout rescue screens nominated the PI3K pathway as a key signaling node that mediates resistance to BET inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107707/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421163
Series		Accession: GSE107707	ID: 200107707

1337. Distinct structural classes of activating FOXA1 alterations in prostate cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 61 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123625/
Series		Accession: GSE123625	ID: 200123625

1338. Distinct structural classes of activating FOXA1 alterations in prostate cancer progression [RNA-Seq]
(Submitter supplied) Expression profiles of 22RV1 prostate cancer cells following FOXA1 genetic engineering and or TLE3 knock-down
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123619/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509422
Series		Accession: GSE123619	ID: 200123619

1339. A novel computational complete deconvolution method using RNA-seq data
(Submitter supplied) The cell type composition of many biological tissues varies widely across samples. Such sample heterogeneity hampers efforts to probe the role of each cell type in the tissue microenvironment. Current approaches that address this issue have drawbacks. Cell sorting or single-cell based experimental techniques disrupt in situ interactions and alter physiological status of cells in tissues. Computational methods are flexible and promising; but they often estimate either sample-specific proportions of each cell type or cell-type-specific gene expression profiles, not both, by requiring the other as input. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 40 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123604/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509361
Series		Accession: GSE123604	ID: 200123604

1340. H1609088 Human RNA-Sequencing
(Submitter supplied) Transcriptome profiling of KYSE30 cells after intracellular invasion by Porphyromonas gingivalis  Purpose: Overabundance of Porphyromonas gingivalis (P. gingivalis) plays oncogenic roles in development and progression of esophageal squamous cell carcinoma (ESCC). To unveil the molecular mechanisms underlying the tumor-promoting role, RNAseq was used to identify differentially expressed genes in response to P. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121995/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA501907
Series		Accession: GSE121995	ID: 200121995

1341. RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by array
Platforms: GPL11154 GPL6801 60 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119337/
Series		Accession: GSE119337	ID: 200119337

1342. RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq]
(Submitter supplied) Alteration in RNA editing has been connected to tumor progression and many other important human diseases. However, the role of RNA editing in intrahepatic cholangiocarcinoma (ICC) remains unclear. Here we conducted a transcriptome-wide investigation in ICCs, and revealed ADAR-associated over-editing occurred uniformly in ICCs. Collectively, these results reveal a previously unrecognized role of RNA editing in malignant transformation into ICC, and ADAR1 inhibition may obviate progression and relapse of this malignancy.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119336/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488803
Series		Accession: GSE119336	ID: 200119336

1343. BRCA2 abrogation triggers innate immune responses potentiated by treatment with PARP inhibitors
(Submitter supplied) Heterozygous germline mutations in BRCA2 predispose to breast and ovarian cancer. Contrary to non-cancerous cells, where BRCA2 deletion causes cell cycle arrest or cell death, BRCA2 inactivation in tumors is associated with uncontrolled cell proliferation. We set out to investigate this conundrum by exploring modalities of cell adaptation to loss of BRCA2 and focused on genome-wide transcriptome alterations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123631/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509430
Series		Accession: GSE123631	ID: 200123631

1344. IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors
(Submitter supplied) Here we explored how cytokines of the tumor milieu, interleukin (IL)-6 and IL-4, interact to influence target gene expression in primary human monocyte-derived macrophages (hMDMs). We show that dual stimulation with IL-4 and IL-6 synergistically modified gene expression. Among the synergistically induced genes are several targets with known pro-tumorigenic properties, such as CC-chemokine ligand 18 (CCL18), transforming growth factor alpha (TGFA) or CD274 (programmed cell death 1 ligand 1 (PD-L1)). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123603/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA509359
Series		Accession: GSE123603	ID: 200123603

1345. High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer
(Submitter supplied) Most triple negative breast cancers (TNBCs) are aggressively metastatic with a high degree of intratumoral heterogeneity. We employed patient-derived xenograft models established from the breast tumors of patients with treatment-naïve metastatic TNBC to study clonal dynamics during metastasis. Genomic sequencing coupled with high-complexity barcode-mediated clonal tracking revealed robust alterations in clonal architecture between primary tumors and corresponding metastases that were deterministic rather than stochastic. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120753/
Series		Accession: GSE120753	ID: 200120753

1346. Phosphorylation of SRSF1 at Tyr-19 promotes cell proliferation in pediatric acute lymphoblastic leukemia
(Submitter supplied) we identified for the first time that the phosphorylation state of SRSF1 is linked to different phases in ALL. Our results underscore the phosphorylation of SRSF1 at the Tyr-19 residue disrupts subcellular localization of SRSF1 and promotes cell proliferation in leukemic cells by accelerating cell-cycle progression. Targeting Tie2 kinase is able to catalyze Tyr-19 phosphorylation of SRSF1, and offer a promising therapeutic target for the treatment of pediatric ALL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118727/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486552
Series		Accession: GSE118727	ID: 200118727

1347. Evaluating pre-clinical models for studying NASH driven HCC.
(Submitter supplied) We sequenced liver biopsy tissue from healthy, patients with NAFLD and patients with NASH
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115193/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474086
Series		Accession: GSE115193	ID: 200115193

1348. Histone demethylase LSD1 is required for germinal center formation and BCL6 driven lymphomagenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 34 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118783/
Series		Accession: GSE118783	ID: 200118783

1349. RNA sequencing of HepG2 cells treated with estradiol or estrogen receptor agonist
(Submitter supplied) We report differential expressed genes in HepG2 cells treated with control, E2, or an ER agonist
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112983/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449680
Series		Accession: GSE112983	ID: 200112983

1350. Gene expression profiling of cutaneous T cell lymphoma cell lines and primary tumor samples treated with mechlorethamine and romidepsin.
(Submitter supplied) In this study, we demonstrated the synergistic effect of the mechlorethamine-romidepsin combination in cutaneous T cell lymphoma cell lines and CD4+ T cells derived from patients with Sezary Syndrome. We identify the signaling pathways specifically perturbed under treatment with mechlorethamine-romidepsin combination.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110248/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433306
Series		Accession: GSE110248	ID: 200110248

1351. Transcriptional changes in lymphoma cells induced by LSD1 depletion
(Submitter supplied) Using RNA-seq we identified the gene expression changes in lymhpoma cells (OCI-Ly1) expressing LSD1 targeted shRNA and control shRNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106416/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416797
Series		Accession: GSE106416	ID: 200106416

1352. Comparative Transcriptomics Unravels Prodigiosin’s Potential Cancer-Specific Activity Between Human Small Airway Epithelial Cells and Lung Adenocarcinoma Cells
(Submitter supplied) Objective: Non-small cell lung cancer (NSCLC) is extremely lethal upon metastasis and requires safe and effective systemic therapies to improve a patient’s prognosis. Prodigiosin (PG) appears to selectively and effectively target cancer but not healthy cells. However, PG’s cancer-specific activity has remained elusive until recently. Methods: PG’s cancer-specific performance was compared to Docetaxel (DTX), Paclitaxel (PTX), and Doxorubicin (DOX) against human lung adenocarcinoma (A549) and human small airway epithelial cells (HSAEC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118448/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485691
Series		Accession: GSE118448	ID: 200118448

1353. RNA-seq of WT and Nocturnin knockout A549 cells
(Submitter supplied) mRNA regulation by the circadian protein Nocturnin in A549 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123477/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508882
Series		Accession: GSE123477	ID: 200123477

1354. Single Cell RNA sequence data from a human ovarian cancer sample
(Submitter supplied) Purpose: Investigate cellular heterogeneity in a fresh human ovarian cancer tissue sample Methods: Enzymatic digestion of fresh tissue sample collected from the operating room to produce single cell suspension. Cells were labelled with fluorescent antibodies to CD3, CD14, CD19, CD20, CD56 and FACS sorted to remove immune cells.  The negative population was used for sequencing. Single cells were processed using the Fluidigm C1 Chip to generate barcoded cDNA for each cell. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 93 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508840
Series		Accession: GSE123476	ID: 200123476

1355. Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner
(Submitter supplied) RNA-seq analysis of BJ cells overexpressing RasV12 and escaping senescence
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123380/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508601
Series		Accession: GSE123380	ID: 200123380

1356. Aging-associated patterns in the expression of human endogenous retroviruses
(Submitter supplied) Human endogenous retroviruses (HERV) are relics of ancient retroviral infections in our genome. Most of them have lost their coding capacity, but proviral RNA or protein have been observed in several disease states (e.g. in inflammatory and autoimmune diseases and malignancies). However, their clinical significance as well as their mechanisms of action have still remained elusive. As human aging is associated with several biological characteristics of these diseases, we now analyzed the aging-associated expression of the individual proviruses of two HERV families, HERV-K (91 proviruses) and HERV-W (213 proviruses) using genome-wide RNA-sequencing (RNA-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122309/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504561
Series		Accession: GSE122309	ID: 200122309

1357. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma
(Submitter supplied) Multiple myeloma (MM), a plasma cell (PC) malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity within and between patients is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply single cell RNA-seq to study the heterogeneity of 40 individuals along the MM progression spectrum. We define malignant PC at single cell resolution, demonstrating high inter-patient variability that can be explained by expression of known MM drivers and additional putative factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 135 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117156/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481319
Series		Accession: GSE117156	ID: 200117156

1358. The splicing factor RBM25 controls MYC activity in Acute Myeloid Leukemia
(Submitter supplied) Cancer sequencing studies have implicated regulators of pre-mRNA splicing as important disease determinants in Acute Myeloid Leukemia (AML), but the underlying mechanisms have remained elusive. We hypothesized that “non-mutated” splicing regulators may also play a role in AML biology and therefore conducted an in vivo shRNA screen in a mouse model of CEBPA mutant AML. This led to the identification of the splicing regulator RBM25 as a novel tumor suppressor, and down-regulation of RBM25 increased proliferation and decreased apoptosis in human leukemic cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114027/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454907
Series		Accession: GSE114027	ID: 200114027

1359. Proteogenomic characterization of human early-onset gastric cancer
(Submitter supplied) We report proteogenomic analysis of diffuse gastric cancers (GCs) in young population. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 160 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122401/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508414
Series		Accession: GSE122401	ID: 200122401

1360. PRMT5 Interacts with the BCL6 Oncoprotein and is Required for Germinal Center Formation and Lymphoma Cell Survival
(Submitter supplied) We have found that PRMT5 methylates BCL6 and is needed for its full transcriptional repressor activity. Concomitant inhibition of both BCL6 and PRMT5 exhibits synergistic killing of BCL6-expressing lymphoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116963/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480701
Series		Accession: GSE116963	ID: 200116963

1361. The combination of cantharidin and anti-angiogenic therapeutics presents synergistic antitumor effects against pancreatic cancer
(Submitter supplied) Background: Cantharidin, an active constituent of mylabris, is believed to have anti-tumor activity. Cantharidin selectively inhibit protein phosphatase 2A (PP2A), a repressor of oncogenic kinase pathways (ERK, JNK, NF-κB, and PKC). Cantharidin represses the growth and metastasis of pancreatic cancer cells in vitro. In the present study, we investigated the effects of cantharidin on pancreatic cancer xenografts in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114040/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA459723
Series		Accession: GSE114040	ID: 200114040

1362. High-throughput RNA sequencing on circular RNA profiles of human triple-negative breast cancer and adjacent normal tissues
(Submitter supplied) In an attempt to search for metastasis-associated circRNAs, we performed RNA-sequencing on ribosomal RNA-depleted total RNA from three pairs of triple-negative breast cancer (TNBC) and adjacent normal tissues. A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Taken together, 69,815 distinct circRNAs were found in this study and 87% were derived from exons, and the others were derived from introns, intergenic region and 3′ or 5′ UTR, etc. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450481
Series		Accession: GSE113230	ID: 200113230

1363. Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma
(Submitter supplied) Glioblastoma is the most common primary malignant brain tumor in adults and associated with poor survival. Standard-of-care chemotherapy and radiation confer a median overall survival of under two years. The Ivy Foundation Early Phase Clinical Trials Consortium conducted a randomized, multi institution clinical trial to evaluate immune responses and survival following neoadjuvant and/or adjuvant therapy with pembrolizumab, a programmed cell death protein 1 (PD-1) monoclonal antibody, in 35 patients with recurrent, surgically resectable glioblastoma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 29 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498500
Series		Accession: GSE121810	ID: 200121810

1364. RNA-sequencing and CRISPR/Cas9 Screen of PEO1 cells grown in suspension.
(Submitter supplied) RNA-sequencing of PEO1 cells grown in suspension (SUS1 and SUS3) was performed to evaluate transcriptional reprogramming during anokis escape. CRISPR/Cas9 screen of PEO1 cells grown in adherent and suspension culture settings for 5 days or 10 days. GeCKO v2 library transduced in PEO1 cell line and cells were selected with puromycin. PEO1 line was authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123290/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA508193
Series		Accession: GSE123290	ID: 200123290

1365. Next Generation Sequencing Facilitates Quantitative Analysis of  Transcriptomes at LncRNA and mRNA and miRNA levels between Hep2 cells with stable transfection of MYCT1 and non-transfection of MYCT1
(Submitter supplied) Purpose: To obtain the differentially expressed LncRNA, mRNAs and miRNAs between the two groups of cells. Results: We identified 174 LncRNAs, 327 mRNAs and 235 miRNAs differentially expressed in MYCT1-overexpressed Hep2 cells compared to the controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123275/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507997
Series		Accession: GSE123275	ID: 200123275

1366. Transcriptional response to PORCN inhibition using an HPAF-II orthotopic model upon MYC perturbation
(Submitter supplied) SRP137043 - PRJNA448654 - Timecourse RNA-seq response to PORCN inhibition using an HPAF-II orthotopic model with different MYC states
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118231/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448654
Series		Accession: GSE118231	ID: 200118231

1367. Transcriptional response to PORCN inhibition using an in vitro model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
(Submitter supplied) SRP136961 - PRJNA448457 - RNA-seq of response to PORCN inhibition, using ETC-159, in vitro of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118190/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448457
Series		Accession: GSE118190	ID: 200118190

1368. Transcriptional response to PORCN inhibition using a subcutaneous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
(Submitter supplied) SRP136970 - PRJNA448481 - RNA-seq of response to PORCN inhibition, using ETC-159,in a subcutanenous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118179/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448481
Series		Accession: GSE118179	ID: 200118179

1369. Transcriptional response to PORCN inhibition using an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
(Submitter supplied) Timecourse RNA-seq of response to PORCN inhibition, using ETC-159, in an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 43 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448521
Series		Accession: GSE118041	ID: 200118041

1370. RNA-Seq in two Ewing sarcoma cell lines: A673 and SKNMC
(Submitter supplied) As the second most common malignant bone tumor in children and adolescents, Ewing sarcoma is initiated and exacerbated by a chimeric oncoprotein, most commonly, EWS-FLI1. In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482316
Series		Accession: GSE117485	ID: 200117485

1371. RNASEQ Analysis of sh-TRC and sh-MIR100HG in the triplex negative breast cancer
(Submitter supplied) Purpose:The goals of this study are using next generation sequencing to identify differentially expressed genes by analyzing knockdown of MIR100HG in triple-negative breast cancer
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107717/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421177
Series		Accession: GSE107717	ID: 200107717

1372. Gene exression in single T cells across division states.
(Submitter supplied) Purpose: To compare diversity of primary human CD8+ T cells that have divided 0, 1, or 2 times on day 3 of ex vivo expansion from naïve resting state. Methods: Naïve T cells were enriched from human peripheral blood monoluclear cells (PBMCs), labeled with CFSE dye, and expanded for 3 days using rapid expansion protocol (Li, Y. & Kurlander, R.J. Journal of Translational Medicine, 2010). On day 3, 10,000 single live CFSE+ CD8+ T cells from each of divisions 0, 1, and 2 were sorted and immediately processed using 10X Genomics single-cell RNA-sequencing platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (CSV, H5) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119139/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488249
Series		Accession: GSE119139	ID: 200119139

1373. Intrahepatic MAIT cell gene expression revealed by RNA-seq
(Submitter supplied) RNA-seq was carried out as described by Simone Picelli et al. with minor modifications (Genome Res 2014;24:2033-40). Briefly, RNA was extracted from 5000 cells using a miRNeasy Micro Kits (Qiagen, German). RNA quality was assessed with an Agilent RNA 6000 Pico Kit (Agilent Technologies, cat#5067-1513, USA) on an Agilent 2100 Bioanalyzer. Each library was prepared from 2ng of total RNA. After reverse transcription, cDNA was amplified for 8 cycles followed by Agencourt AMPure XP purification, the quality of cDNA library was checked on an Agilent High Sensitivity DNA Kit (Agilent Technologies, cat#5067-4626). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 15 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117627/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482707
Series		Accession: GSE117627	ID: 200117627

1374. Intermittent Drug Treatment of BRAFV600E Melanoma Cells Delays Resistance by Sensitizing Cells to Rechallenge
(Submitter supplied) Melanoma patients receiving drugs targeting BRAFV600E and MKK1/2 invariably develop resistance and continue progression, limiting the efficacy of treatment.  As an alternative to continuous dosing schedules, intermittent treatment strategies involving intervening periods of drug withdrawal have been proposed to delay resistance. The efficacy of this treatment strategy has been supported by preclinical findings and several clinical case reports. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117123/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481166
Series		Accession: GSE117123	ID: 200117123

1375. LHX9 rescues KRAS suppression through transcriptional regulation of YAP1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 14 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116824/
Series		Accession: GSE116824	ID: 200116824

1376. LHX9 rescues KRAS suppression through transcriptional regulation of YAP1 [RNA-Seq]
(Submitter supplied) Oncogenic KRAS signaling is required for tumor survival in cancers that harbor KRAS mutations. We recently performed a genome-scale expression screen to identify genes that bypass KRAS dependency. Here we demonstrate that the developmental transcription factor LHX9 rescues KRAS suppression in vitro and xenograft models. Furthermore, LHX9 decreases cell sensitivity to KRASG12C and MEK1/2 inhibitors. LHX9 promotes transcriptional changes associated with KRAS. Importantly, YAP1 upregulation by LHX9 is required for the rescue of KRAS suppression. Together we identify LHX9 as a YAP1 transcriptional regulator that permits KRAS-dependent cells to proliferate without KRAS expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116823/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480295
Series		Accession: GSE116823	ID: 200116823

1377. NK cell-mediated cytotoxicity contributes to tumor control by a cytostatic drug combination
(Submitter supplied) Accumulating evidence suggests that molecularly targeted therapies, which were originally developed to target  the underlying cell autonomous genetic drivers of tumorigenesis, can provoke tumor specific immune  responses. Using immunocompetent mouse models of KRAS mutant lung adenocarcinoma, we show that a  combination of MEK and CDK4/6 inhibitors can induce natural killer (NK) cell immune surveillance that is  necessary for its full anti-tumor effect. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 57 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433624
Series		Accession: GSE110397	ID: 200110397

1378. Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees
(Submitter supplied) Intrahepatic cholangiocarcioma has two molecular classification of intrahepatic CCA with distinct clinical, pathological, biological and prognostic differences
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 57 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107943/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422089
Series		Accession: GSE107943	ID: 200107943

1379. Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL15456 GPL20301 GPL10558 41 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107782/
Series		Accession: GSE107782	ID: 200107782

1380. Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator [RNA-seq]
(Submitter supplied) EZH2 induces active transcription of the AR gene, thereby increasing AR level and promoting AR signaling. Importantly, EZH2-mediated activation of AR requires EZH2 protein occupancy at the AR gene promoter, but is independent of PRC2 as well as its histone methyltransferase activity
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107781/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421358
Series		Accession: GSE107781	ID: 200107781

1381. Transcriptome analysis identifies the dysregulation of ultraviolet target genes in human skin cancers
(Submitter supplied) In this study, we performed RNA-Seq studies to generate a transcriptomic cohort containing UV-responsive genes in human skin cells exposed to different UVR conditions. We then performed rigorous bioinformatics analysis to define a UV gene expression signature that is conserved among cells from different donors. We further demonstrated that the UV signature genes are significantly enriched in genes dysregulated in human skin squamous cell carcinomas.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85443/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338465
Series		Accession: GSE85443	ID: 200085443

1382. RNA-seq and microRNA-seq reveal RNAs and microRNAs under the regulation of miR-125b in NCCIT tumor cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL23227 18 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123157/
Series		Accession: GSE123157	ID: 200123157

1383. RNA-seq reveals RNAs under the regulation of miR-125b in NCCIT tumor cells
(Submitter supplied) To investigate the role and mechanism of miR-125b on NCCIT cells without bias, we analyzed differentially expression RNA profile among miR-125b antagomir-, miR-125b agomir-, and negative control-transfected NCCIT tumor cells by RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 9 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123113/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507586
Series		Accession: GSE123113	ID: 200123113

1384. EnD-Seq and AppEnD: Sequencing 3' ends to identify non-templated tails and degradation intermediates
(Submitter supplied) Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3’ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3’ ends contain posttranscriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3’ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497386
Series		Accession: GSE121461	ID: 200121461

1385. RNA-seq profiling of trastuzumab or lapatinib sensitive and resistant SKBR3 breast cancer cells
(Submitter supplied) RNAseq was done using Library protocol =Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection , HiSeq 101 Cycle Paired-End Sequencing v4
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114575/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471825
Series		Accession: GSE114575	ID: 200114575

1386. Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of armadillo repeat containing 12 (ARMC12)
(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of a public microarray dataset, we identified armadillo repeat containing 12 (ARMC12) as a novel ARM member associated with the progression of NB. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107516/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420394
Series		Accession: GSE107516	ID: 200107516

1387. A chemical probe for Tudor domain protein SPIN1 to investigate chromatin functions
(Submitter supplied) Lysine and arginine methylation are amongst the most frequent modifications on unstructured histone tails and in combination with other modifications provide the basis for a combinatorial 'chromatin or histone code'. Recognition of modified histone residues is accomplished in a specific manner by 'reader' domains that recognize chromatin modifications allowing to associate with specific effector complexes mediating chromatin functions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123084/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507454
Series		Accession: GSE123084	ID: 200123084

1388. mRNA expression profile in MHCC-97H-SH-NC And MHCC-97H-SH-UCK2 liver cancer cells
(Submitter supplied) To study the mRNA modulating network and different expressed mRNA lists in MHCC-97H-SH-UCK2 cells, we use high-throughout method to genomically detect the expression profile of mRNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123039/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507372
Series		Accession: GSE123039	ID: 200123039

1389. 2-5A-Mediated mRNA Decay and Transcription Act in Concert to Reprogram Protein Synthesis during dsRNA Response
(Submitter supplied) RNA degradation by RNase L during 2-5A-mediated decay (2-5AMD) is a conserved mammalian stress response to viral and endogenous double-stranded RNA (dsRNA). To understand this mechanism we examined 2-5AMD in human cells by spike-in RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123034/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507354
Series		Accession: GSE123034	ID: 200123034

1390. Enhancer profiling of chronic lymphocytic leukemia cells
(Submitter supplied) Enhancer  profiling has emerged as a powerful approach for discovering the cis-regulatory elements that define transcriptional core regulatory circuits. Characteristic biochemical and biophysical attributes of chromatin mark active enhancer elements, which can be leveraged with genome-wide assay technologies for discovery. This includes chromatin immunoprecipitation followed by sequencing (ChIP-seq) for histone H3 acetylated lysine 27 (H3K27ac). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 36 Samples
FTP download: GEO (BEDGRAPH, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490189
Series		Accession: GSE119744	ID: 200119744

1391. TGFβ1-mediated functional inhibition of mesenchymal stromal cells in MDS and AML
(Submitter supplied) Mesenchymal stromal cells (MSC) are involved in the pathogenesis of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), but how they contribute to the expansion of malignant cells and hematopoietic failure is poorly understood. To further characterize the pathological phenotype we performed RNA sequencing of MSC from patients with MDS and AML. Data analysis revealed a specific molecular signature with a significant overlap of genes commonly deregulated in all MDS subtypes and in AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107490/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420350
Series		Accession: GSE107490	ID: 200107490

1392. AhR activity directs BRAF inhibitors resistance in metastastic melanoma
(Submitter supplied) BRAF oncogene is mutated in ~50% of human cutaneous melanomas. The BRAF V600E mutation leads to constitutive activation of the mitogen-activated protein kinase (MAPK) pathway fuelling cancer growth. The inhibitors of BRAF V600E (BRAFi), lead to massive and high response rate. However, BRAFi-resistant cells that operate as a cellular reservoir for relapses severely limits the duration of the clinical response. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104869/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414069
Series		Accession: GSE104869	ID: 200104869

1393. Single-cell Multi-omics Sequencing and Analyses of Human Colorectal Cancer
(Submitter supplied) Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multi-omics sequencing together with multi-regional sampling of the primary tumor, lymphatic and distant metastases, we provide insights beyond intratumoral heterogeneity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL20301 2503 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382695
Series		Accession: GSE97693	ID: 200097693

1394. mRNA sequencing of oropharyngeal cancer cell lines
(Submitter supplied) mRNA sequencing was performed on oropharyngeal cancer cell lines including 4 HPV-positive and 4 HPV-negative lines. Two lines  (CUOP2 and CUOP3) were newly derived from HPV-positive tonsil cancers (derivation is described in "Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus" by Pirotte et al. This work was undertaken with the aims of quantifying levels of HPV gene transcription and identifying human:viral fusion transcripts arising from integrated viral sequences. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123029/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507280
Series		Accession: GSE123029	ID: 200123029

1395. A global identification of PUM1 and PUM2 mRNA targets and their protein cofactors in human seminoma TCam-2 cells
(Submitter supplied) The functions of human PUM1 and PUM2 are considered to be redundant given that both PUF1 and PUF2 recognize the same PBE motif UGUANAUA.  However pools of mRNAs published so far for PUM1 and PUM2 do not overlap. Therefore we sought to investigate the issue of redundancy in human cells. The both PUM proteins are less conserved in the region that is outside the PUM domain. We sought that interactors could be different. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20301 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA507255
Series		Accession: GSE123016	ID: 200123016

1396. Genes regulated in HT-1080 cells after treatment with IRAK4 inhibitor
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122912/
Series		Accession: GSE122912	ID: 200122912

1397. Concomitant BCORL1 and BRAF mutations in vemurafenib-resistant melanoma cells
(Submitter supplied) BRAF is the most frequently mutated gene in melanoma. Constitutive activation of mutant BRAFV600E leads to aberrant Ras-independent MAPK signaling and cell transformation. Inhibition of mutant BRAF is a current front-line therapy for such cases, with improved survival compared with chemotherapy. Unfortunately, reactivation of MAPK signaling by several mechanisms has been shown to cause drug resistance and disease recurrence. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 9 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107370/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419913
Series		Accession: GSE107370	ID: 200107370

1398. Gene expression from laser capture microdissected pancreatic cancer epithelium and stroma
(Submitter supplied) This study used laser capture microdissection to obtain paired tumor epithelium and stroma RNA samples from human pancreatic ductal adenocarcinoma (PDA) frozen sections. Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads. These data were used to model compartment-specific gene expression density on a genome-wide scale and build an algorithm for transcriptional devonvolution (ADVOCATE). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 204 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360619
Series		Accession: GSE93326	ID: 200093326

1399. Transcriptomic analysis of MERS-CoV infected Calu-3 cell with or without AM580 treatment
(Submitter supplied) We report a broad spectrum antiviral drug AM580, RNA-Seq technology was used to compare the host gene mRNA expression between different groups to indicate the host pathway changes upon MERS-CoV infection and AM580 treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506733
Series		Accession: GSE122876	ID: 200122876

1400. Genes regulated in HT-1080 cells after 24 hours of treatment with IRAK4 inhibitor
(Submitter supplied) Analysis of HT-1080 fibrosarcoma cells transcriptome following  24 hours treatment with IRAK4 inhibitor was performed.  Results provide insight into mode of action of IRAK4 inhibitor under study. Project co-financed from European Regional Development Fund under The Operational Program Innovative Economy, 2007-2013, measure 1.4 (UDA-POIG.01.04.00-12-049/11-00)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122845/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506657
Series		Accession: GSE122845	ID: 200122845

1401. Genes regulated in HT-1080 cells after 4 hours of treatment with IRAK4 inhibitor
(Submitter supplied) Analysis of HT-1080 fibrosarcoma cells transcriptome following 4 hours treatment with IRAK4 inhibitor was performed.  Results provide insight into mode of action of IRAK4 inhibitor under study. Project co-financed from European Regional Development Fund under The Operational Program Innovative Economy, 2007-2013, measure 1.4 (UDA-POIG.01.04.00-12-049/11-00)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506658
Series		Accession: GSE122844	ID: 200122844

1402. Next-generation RNA sequencing to determine changes in gene expression during breast cancer progression
(Submitter supplied) Purpose: The goal of the study is to compare NGS-derived transcriptome in an isogenic breast cancer progression model cell line system. By comparing the protein-coding and noncoding gene expression of normal versus tumorigenic breast cancer cell lines, we will be able to identify genes that show aberrant expression during breast cancer progression. Methods: We isolated poly A + RNA from four isogenic mammary epithelial cell lines showing various stages of breast cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494563
Series		Accession: GSE120796	ID: 200120796

1403. Expression profiling of pancreatic adenocarcinoma and ductal adenocarcinoma cell lines.
(Submitter supplied) We characterized baseline gene expression profiles for eleven human pancreatic adenocarcinoma and ductal adenocarcinoma cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122818/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506428
Series		Accession: GSE122818	ID: 200122818

1404. RNA Sequencing of three pairs of gastric cancer
(Submitter supplied) The prognosis after curative resection of gastric cancer (GC) remains unsatisfactory, and thus, the development of treatments involving alternative molecular and genetic targets is critical. Circular RNAs (circRNAs), new stars of the non-coding RNA network, have been identified as critical regulators in various cancers. Here, we aimed to determine the circRNA expression profile and investigate the functional and prognostic significance of circRNA in GC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506381
Series		Accession: GSE122796	ID: 200122796

1405. Acetylation of spliceosome protein PHF5A modulates stress responses and colorectal carcinogenesis through alternative splicing mediated upregulation of KDM3A
(Submitter supplied) The process utilized by cancer cells for adapting to cellular stress is a key point for carcinogenesis. Alternative pre-mRNA splicing induced post-transcriptional gene expression regulation is one of the pathways for tumors maintaining proliferation rates accompanying the malignant phenotype under stress. However, the protein post-translational modification, especially protein acetylation on pre-mRNA splicing processes under stress is unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122761/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506256
Series		Accession: GSE122761	ID: 200122761

1406. Single cell RNA-seq profiles of primary, metastatic, drug-resistant and drug-holiday cells
(Submitter supplied) We employed Single cell RNA-seq to identify the transcriptome of cisplatin sensitive, resistant and drug-holiday cells from patient-derived OSCC cells isolated from primary and metastatic sites.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1431 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483471
Series		Accession: GSE117872	ID: 200117872

1407. Mitochondrial hypoxic stress induces RNA editing by APOBEC3G in lymphocytes
(Submitter supplied) Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes/macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Here we show that the related APOBEC3G cytidine deaminase induces site-specific C-to-U RNA editing in natural killer (NK), CD8+ T cells and lymphoma cell lines upon cellular crowding and hypoxia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471680
Series		Accession: GSE114519	ID: 200114519

1408. Integrated Genetic and Proteomic Analysis Identifies PLK1 as a Candidate Therapeutic Target for SETD2-Deficient Clear Cell Renal Cell Carcinoma
(Submitter supplied) We systematically analyzed the alterations in histone epigenetic marks (H3K36me3 and H4K16ac), mRNA transcriptome evoked by SETD2 depletion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 14 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107391/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419954
Series		Accession: GSE107391	ID: 200107391

1409. Transcriptome of U251 cells overexpression complement component 7
(Submitter supplied) We identified a rare coding variant (p.K420Q) in the complement component 7 (C7) gene affecting the risk of Alzheimer's disease. To investigate the cellular effects of the mutant, we performed RNA-seq in cell line overexpression wilt-type and mutant C7.   U251 glioma cells with stable expression of mutant APP (K670N/M671L) (U251-APP cells), which produce Aβ42 under Dox inducing, were used as the model cell. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101608/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394980
Series		Accession: GSE101608	ID: 200101608

1410. Estradiol-regulated Dependence Receptor UNC5A Restricts Estradiol Signaling and Luminal to Basal Transition and Metastasis of Breast Cancer
(Submitter supplied) Estrogen receptor alpha (ERα)-positive breast cancers, while initially being responsive, eventually develop resistance to ERα targeted therapies through ERα-dependent and ERα-independent mechanisms.  Through functional genomic studies we report heretofore unrecognized role for the axon guidance dependence receptor UNC5A in fine-tuning estradiol (E2) and anti-estrogen response.  Knockdown of the estradiol-inducible UNC5A caused unrestricted ERα signaling as evident from deregulated E2-regulated gene expression and E2-independent tumorigenesis accompanied with multi-organ metastatic spread in xenograft models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 16 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89700/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352975
Series		Accession: GSE89700	ID: 200089700

1411. RNA sequencing data in AGS-BX1 cells treated with C7
(Submitter supplied) C7 is a novel lytic cycle inducer of Epstein-Barr virus (EBV) in EBV-positive epithelial cells. To analyze the potential signaling pathways that are activated by C7 for induction of EBV lytic cycle, we performed a RNA sequencing to analyze the RNA expression profiles in AGS-BX1 gastric carcinoma cells before and after treatment with C7.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122751/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506238
Series		Accession: GSE122751	ID: 200122751

1412. Dynamic molecular monitoring reveals that SWI/SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 14 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122513/
Series		Accession: GSE122513	ID: 200122513

1413. Dynamic molecular monitoring reveals that SWI/SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma [RNA-Seq]
(Submitter supplied) Ibrutinib plus venetoclax is a highly effective combination in mantle cell lymphoma. However, strategies to enable the evaluation of therapeutic response are required. Our prospective analyses of patients within the AIM study revealed genomic profiles that clearly dichotomized responders and non-responders. Mutations in ATM were present in most patients who achieved a complete response, while chromosome 9p21.1-p24.3 loss and/or mutations in components of the SWI/SNF chromatin remodeling complex were present in all patients with primary resistance and 2/3 patients with relapsed disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122509/
Series		Accession: GSE122509	ID: 200122509

1414. Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
(Submitter supplied) G-quadruplexes (G4) are secondary nucleic acid structures that have been associated with genomic instability and cancer progression. When present in the promoter of some oncogenes, G4 structures can affect gene regulation and, hence, represent a possible therapeutic target. In this study, RNA-Seq was used to explore the effect of a G4-binding anthraquinone derivative, named AQ1, on the whole-transcriptome profiles of two common cell models for the study of KIT pathways; the human mast cell leukemia (HMC1.2) and the canine mast cell tumor (C2). more...
Organism:	Homo sapiens; Canis lupus familiaris
Type:		Expression profiling by high throughput sequencing
Platforms: GPL24229 GPL20301 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120272/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492338
Series		Accession: GSE120272	ID: 200120272

1415. RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.
(Submitter supplied) Purpose: Detailed exploration of de novo Fatty Acid Synthesis (DNFA) transcription regulation and clinical relevance in melanomas. This study was designed to achieve the following goals: 1) determine the impact of SREBP1 depletion on gene expression in metastatic melanoma cells; 2) determine the specificity of ASO and other reagents inhibiting SREBF1 mRNA.  Method: RNA-Seq was performed after culture with control and various SREBF1-depleting agents, including pooled siRNAs and individual ASOs, in HT-144 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122707/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506045
Series		Accession: GSE122707	ID: 200122707

1416. Receptor tyrosine kinase signaling promotes post-embryonic morphogenesis and survival of glia and neural progenitor cells
(Submitter supplied) Glioblastomas (GBMs), which are the most deadly malignant brain tumors of children and adults, infiltrate the brain and grow rapidly, and are resistant to current therapies. Glioblastomas (GBMs) frequently display mutations that activate receptor tyrosine kinases (RTKs), such as EGFR, which are thought to cooperate with additional factors to drive tumorigenesis. To identify and characterize genetic pathways that cooperate with RTKs to drive GBM progression, we performed RNA sequencing on several cell cultures created from surgical specimens from tumors with alterations in RTKs, and these cultures were grown as neurospheres in serum-free media used for normal neural stem/progenitor cell cultures. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122679/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA506003
Series		Accession: GSE122679	ID: 200122679

1417. Telomere-Dependent and Telomere-Independent Roles of RAP1 in Regulating Human Stem Cell Homeostasis
(Submitter supplied) RAP1 is well known as a telomere-binding protein; yet its functions in human stem cells remain unclear. Here we generated RAP1-deficient human embryonic stem cells (hESCs) by CRISPR/Cas9 and obtained RAP1-deficient human mesenchymal stem cells (hMSCs) and neural stem cells (hNSCs) via directed differentiation. In both hMSCs and hNSCs, RAP1 negatively regulated telomere length. In addition, RAP1 acted as a transcriptional regulator of RLEN by tuning the methylation status of its promoter region. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20795 12 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122654/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505881
Series		Accession: GSE122654	ID: 200122654

1418. Single-Cell Transcriptome Analysis Reveals Estrogen Signaling Coordinately Augments One-Carbon, Polyamine, and Purine Synthesis in Breast Cancer [II]
(Submitter supplied) Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating the estrogen receptor α (ERα). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular responses, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ERα regulates transcription in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 39 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119455/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488528
Series		Accession: GSE119455	ID: 200119455

1419. Homolog-selective degradation as a strategy to probe the function of CDK6 in AML
(Submitter supplied) The design of selective small-molecules is often stymied by similar ligand binding pockets. Here we report the first cyclin-dependent kinase 6 (CDK6) degrader, BSJ-03-123, that uses phthalimide-conjugation to exploit protein-interface determinants to achieve proteome-wide degradation selectivity.  Pharmacologic CDK6 degradation targets a selective dependency of acute myeloid leukemia cells, and coupling acute degradation with transcriptomics and phosphoproteomics enabled dynamic mapping of the immediate role of CDK6 in coordinating signaling and transcription.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116187/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477657
Series		Accession: GSE116187	ID: 200116187

1420. Loss of the Chr16p11.2 candidate gene QPRT leads to aberrant neuronal differentiation
(Submitter supplied) Background: Altered neuronal development is discussed as underlying pathogenic mechanism of Autism Spectrum Disorders (ASD). Copy number variations of 16p11.2 have recurrently been identified in individuals with ASD. Of the 29 genes within this region quinolinate phosphoribosyltransferase (QPRT) showed the strongest regulation during in-vitro neuronal differentiation. We hypothesized a causal relation between this tryptophan related enzyme and neuronal differentiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113734/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453802
Series		Accession: GSE113734	ID: 200113734

1421. Single-Cell Transcriptome Analysis Reveals Estrogen Signaling Coordinately Augments One-Carbon, Polyamine, and Purine Synthesis in Breast Cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 189 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107864/
Series		Accession: GSE107864	ID: 200107864

1422. Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (T47D)
(Submitter supplied) Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating the estrogen receptor α (ERα). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular responses, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ERα regulates transcription in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418867
Series		Accession: GSE107863	ID: 200107863

1423. Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (MCF7)
(Submitter supplied) Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating the estrogen receptor α (ERα). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular responses, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ERα regulates transcription in breast cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 93 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107858/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418865
Series		Accession: GSE107858	ID: 200107858

1424. Combinatory RNA sequencing analyses reveal RNA editing-dependent and -independent gene regulation by ADAR1 in gastric cancer
(Submitter supplied) To investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing were performed in AGS and MKN-45 cells with stable ADAR1 knock-down. Changed frequencies of editing and messenger RNA (mRNA) and microRNA (miRNA) expression were then identified by bioinformatic analyses.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106874/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418301
Series		Accession: GSE106874	ID: 200106874

1425. RB tumor suppressor promotes cancer immunity through downregulating PD-L1 expression
(Submitter supplied) Aberrant expression of immune checkpoint protein programmed death ligand-1 (PD-L1) promotes immune tolerance in cancer. RB is a tumor suppressor known to regulate the cell cycle, DNA damage response, and differentiation. Here, we demonstrate transient knockdown or homozygous deletion of RB markedly induces PD-L1 mRNA expression. RB binds to NFκB protein p65 and serine-249/threonine-252 (S249/T252) phosphorylation of RB is important for its interaction with p65 and suppression of PD-L1 expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109724/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431800
Series		Accession: GSE109724	ID: 200109724

1426. Impact of CD22 CAR T-cell therapy on leukemia cell transcriptome
(Submitter supplied) Although CD19 CAR T therapy has attained encouraging clinical outcomes worldwide, leukemia relapse after this therapy is associated with particular poor prognosis and has become an urgent problem to be solved. In consideration of the possible genetic or transcriptomic mechanisms underlying relapse, leukemia samples before CAR T cell infusion and after relapse were subjected to transcriptome sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122659/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA505889
Series		Accession: GSE122659	ID: 200122659

1427. Molecular Signatures of Multiple Myeloma Progression through Single Cell RNA-Seq
(Submitter supplied) Multiple myeloma (MM) is a malignant plasma cell disorder with well-defined clonal genetic/cytogenetic abnormalities.  However, cellular heterogeneity is a key factor in MM’s progression, therapeutic decision, and response to treatment. Single cell whole transcriptome profiling (scRNA-Seq) offers an opportunity to dissect this molecular heterogeneity during MM progression to better understand the disease and guide rational therapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 597 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118900/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487220
Series		Accession: GSE118900	ID: 200118900

1428. Transcriptome analysis of control and miR-200a overexpressed TF-1 cells
(Submitter supplied) RNA-seq and analysis was perfprmed was performed to identify the affection caused by miR-200a overexpression in TF-1 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA302392
Series		Accession: GSE75082	ID: 200075082

1429. Gene expression analysis of head and neck squamous cell carcinoma (HNSCC) cell lines.
(Submitter supplied) Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESC) cell lines separately, we performed genomic, viral gene expression, and viral integration analyses on 74 cell lines that include all readily-available HPV-positive (9 HNSCC, 8 CESC) and CESC (8 HPV-positive, 2 HPV-negative) cell lines and 55 HPV-negative HNSCC cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 74 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122512/
Series		Accession: GSE122512	ID: 200122512

1430. TNF response in promyelocytic and granulocytic forms of HL60/S4 cells
(Submitter supplied) The human promyelocytic cell line HL60/S4 can be differentiated into a granulocytic form with the addition of all-trans retinoic acid for 4 days. We investigated the conserved and differentiated responses to TNF in the granulocytic and promyelocytic forms of HL60/S4 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120579/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493630
Series		Accession: GSE120579	ID: 200120579

1431. The expression profiles of CD4low(HLA-G+) T cells
(Submitter supplied) The aim of the dataset was to demonstrate that CD4low T cells were murine homolog of CD4lowHLA-G+ T cells by comparing the expression profiles of CD4lowHLA-G+ T cells in prostate cancer (PCa) patients to those of CD4low T cells in PCa mouse models.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20795 GPL21273 8 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432170
Series		Accession: GSE109844	ID: 200109844

1432. Development of Specific Covalent MALT1 Inhibitors and Biomarkers for B-cell Lymphomas
(Submitter supplied) The MALT1 paracaspase plays an essential role in Activated B-cell like Diffuse Large B-cell Lymphoma (ABC DLBCL) downstream of B-cell and Toll-like receptor pathway genes mutated in these tumors. Although MALT1 is considered to be a compelling therapeutic target, development of tractable and specific MALT1 protease inhibitors has thus far been elusive. Herein, we developed a target engagement assay that provides a quantitative readout for specific MALT1 inhibitory effects in living cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108293/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427102
Series		Accession: GSE108293	ID: 200108293

1433. Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [SLAM-Seq]
(Submitter supplied) Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495599
Series		Accession: GSE121070	ID: 200121070

1434. Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [NALM6 RNA-Seq]
(Submitter supplied) Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495597
Series		Accession: GSE121065	ID: 200121065

1435. TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma
(Submitter supplied) The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL11154 GPL18573 92 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115463/
Series		Accession: GSE115463	ID: 200115463

1436. TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (RNA-seq)
(Submitter supplied) The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 GPL19057 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115462/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475110
Series		Accession: GSE115462	ID: 200115462

1437. Gene expression profiles of PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma
(Submitter supplied) We report the gene expression profiles of FACS-sorted PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111389/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436904
Series		Accession: GSE111389	ID: 200111389

1438. A CHAF1B-dependent molecular switch in hematopoiesis and leukemia pathogenesis
(Submitter supplied) CHAF1B is the p60 subunit of the chromatin assembly factor (CAF1) complex, which is responsible for assembly of H3.1/H4 heterodimers at the replication fork during S phase. Here we report that CHAF1B is required for normal hematopoiesis while its overexpression promotes leukemia. CHAF1B has a pro-leukemia effect by binding chromatin at discrete sites and interfering with occupancy of transcription factors that promote myeloid differentiation, such as CEBPA. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 50 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120063/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491485
Series		Accession: GSE120063	ID: 200120063

1439. The splicing factor SRSF1 regulates the radio-resistance of cancer cells through modulating the alternative splicing of PTPMT1
(Submitter supplied) RNA-seq was performed on H1299 cells that stably knocking down SRSF1 or control, as well as these cells that were treated with ionizing radiation, in order to profile the alternative splicing events that were regulated by SRSF1 upon ionizing radiation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107224/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419389
Series		Accession: GSE107224	ID: 200107224

1440. Transcriptomic analysis of acute mitochondrial pyruvate carrier inhibition using UK5099 in ABL prostate cancer cells
(Submitter supplied) ABL cells (derivative of LNCaP) were treated with 100µM UK5099 or vehicle (control) for 72 hours, at which time total RNA was collected and analyzed using RNA-sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472341
Series		Accession: GSE114708	ID: 200114708

1441. Transcriptome-wide identification of transient RNA G-quadruplexes in human cells
(Submitter supplied) We report here on G4RP-seq, which comprises of a cross-linking step, followed by chemical-affinity capture with the G4-specific small-molecule, BioTASQ and target identification using sequencing. This allows for capturing global snapshots of relative average levels of transiently folded G4-RNAs. We observed widespread G4-RNA targets indicative of transient G4 formation in several RNA entities in living human cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112898/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449395
Series		Accession: GSE112898	ID: 200112898

1442. MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 34 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117408/
Series		Accession: GSE117408	ID: 200117408

1443. MYC protein interactome profiling reveals functionally distinct regions that cooperate to drive tumorigenesis (RNA-Seq)
(Submitter supplied) MYC is a potent oncogene associated with aggressive disease in many distinct tumor types. Transforming members of the MYC family (MYC, MYCL1, MYCN) encode transcription factors containing six highly conserved regions, termed MYC homology Boxes (MBs). Here, we conduct proteomic profiling of the MB interactomes, demonstrating that half of MYC interactors require one or more MBs for binding. Comprehensive phenotypic analyses revealed that two MBs are universally required for transformation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 32 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481996
Series		Accession: GSE117407	ID: 200117407

1444. RNA sequencing of GLO1-depleted MDA-MB-231 breast cancer cells
(Submitter supplied) We reported the expression of a pro-metastatic signature in GLO1-depleted MDA-MB-231 cells compared to control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122229/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA504031
Series		Accession: GSE122229	ID: 200122229

1445. Genome wide expression change by RNF168 knocking down in MCF-7 cells
(Submitter supplied) We aim to the investigate the role of RNF168 in breast cancer progression. MCF-7 cells were used as the model and RNF168 was silenced by siRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106617/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417460
Series		Accession: GSE106617	ID: 200106617

1446. Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells
(Submitter supplied) Using RNA-seq to identify gene expression changes after genetic deletion of ADAR
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503859
Series		Accession: GSE122168	ID: 200122168

1447. Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Expression profiling by array; Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing
5 related Platforms 382 Samples
FTP download: GEO (BED, BIGWIG, BW, CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121723/
Series		Accession: GSE121723	ID: 200121723

1448. Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - tumour rRNA-depleted total ssRNAseq data
(Submitter supplied) Glioblastoma in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA methylation and RNA expression data. Tumour subtype transitions commonly occur during the treatment of glioblastoma patients, and transitions to the mesenchymal (MES) subtype have been associated with therapy resistance and adverse prognosis. Here, we generate DNA methylome and histone modification data of glioblastoma primary tumours and show that glioblastoma subtypes differ by their enhancer landscapes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 64 Samples
FTP download: GEO (BIGWIG, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121720/
Series		Accession: GSE121720	ID: 200121720

1449. Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line RNAseq experiments
(Submitter supplied) Glioblastoma in adult patients are classified into four subtypes, IDH, MES, RTK I, and RTK II, based on DNA methylation and RNA expression data. Tumour subtype transitions commonly occur during the treatment of glioblastoma patients, and transitions to the mesenchymal (MES) subtype have been associated with therapy resistance and adverse prognosis. Here, we generate DNA methylome and histone modification data of glioblastoma primary tumours and show that glioblastoma subtypes differ by their enhancer landscapes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121717/
Series		Accession: GSE121717	ID: 200121717

1450. RNAseq analysis of ruxolitinib treated breast cancers
(Submitter supplied) We performed RNA sequencing analysis on fresh-frozen biopsies of metastatic triple-negative breast cancer prior to undergoing therapy with ruxolitinib, or after 2 cycles of therapy in a subset of patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107000/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418761
Series		Accession: GSE107000	ID: 200107000

1451. A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 75 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113042/
Series		Accession: GSE113042	ID: 200113042

1452. A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [RNA-seq]
(Submitter supplied) Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely unknown. Here, we comprehensively map complex assemblies on chromatin and find that ncBAF uniquely localizes to CTCF sites and promoters. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449854
Series		Accession: GSE113041	ID: 200113041

1453. Transcript analysis of multi-locus sampled tumor tissue in patients with non-small cell lung cancer
(Submitter supplied) we investigated the spatial features of surgically-removed biopsies from multiple loci in tumor masses of 15 patients with non-small cell lung cancer (NSCLC). We observed that the immune microenvironment is highly spatial heterogeneous such that intra-tumoral regional variation is as large as inter-personal variation. While the local mutational burden was associated with local T cell clonal expansion, observed local anti-tumor cytotoxicity is strongly associated with local tumoral circumstance rather than TMB alone
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 45 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112996/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449697
Series		Accession: GSE112996	ID: 200112996

1454. Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency
(Submitter supplied) It is important to understand how cells can maintain and exit human pluripotency. We exploited the metabolic and epigenetic differences between naïve and primed pluripotent cells to design a CRISPR-Cas9 screen for identifying genes that promote the exit from naïve pluripotency. Among the known and novel regulators of this early step of human development, we identified the tumor suppressor folliculin (FLCN). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122118/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503630
Series		Accession: GSE122118	ID: 200122118

1455. Loss of the FAT1 tumor suppressor promotes resistance to CDK4/6 inhibitors via the Hippo pathway
(Submitter supplied) Loss of FAT1 promotes resistance to CDK4/6 inhibitors. This study was to compare the differential mRNA expression of FAT1 crispr cells with parental cells, to identify the underlying mechanisms of resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122088/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503479
Series		Accession: GSE122088	ID: 200122088

1456. Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq
(Submitter supplied) Here we investigated different cell populations within ovarian cancer using single-cell RNA seq: fourteen samples from nine patients with differing grades (high grade, low grade and benign) as well as different origin sites (primary and metastatic tumor site, ovarian in origin and fallopian in origin).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118828/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486915
Series		Accession: GSE118828	ID: 200118828

1457. Generic drug screen identifies paracetamol as 5-aza-2’-deoxycytidine sensitizer in head and neck squamous cell carcinoma cells
(Submitter supplied) Aberrant DNA methylation (5mC) is one of the key characteristics of many cancers including head and neck squamous cell carcinoma (HNSCC). The DNA demethylating agent 5-aza-2’-deoxycytidine (DAC) has anti-cancer therapeutic potential, but its clinical efficacy is currently hindered by dose-limiting side effects. Here we investigated the potential use of DAC in the treatment of HNSCC and show that its efficacy is primarily dependent on the ability of DAC to demethylate DNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110045/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432654
Series		Accession: GSE110045	ID: 200110045

1458. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling
(Submitter supplied) We present sc-FTDseq, a microchip platform for single-cell freeze-thaw lysis directly toward 3’ mRNA sequencing. It offers format flexibility with a much simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and the cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in RNA fragmentation, turns out to be fully compatible with single-cell 3’ mRNA sequencing, which detects only ~50 bases at the 3’ end. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL22245 GPL17021 9 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431313
Series		Accession: GSE109535	ID: 200109535

1459. ARv7 represses tumor suppressors genes in castration-resistant prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 100 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106561/
Series		Accession: GSE106561	ID: 200106561

1460. ARv7 represses tumor suppressors genes in castration-resistant prostate cancer  [RNA-Seq]
(Submitter supplied) Endocrine therapies in prostate cancer (PCa) treatment block androgen receptor (AR) function, but are palliative as tumors progress to a lethal, castration-resistant state (CRPC). CRPC remains dependent on AR signaling, which can act through the full-length AR (ARfl) or constitutively active splice variants, e.g. ARv7. We show here that both ARfl and ARv7 bind to the same genomic region and heterodimerize in a CRPC cell line model, but regulate distinct transcriptomes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 120 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417254
Series		Accession: GSE106560	ID: 200106560

1461. Transcriptional profiling of MDA-MB-231 and its ρ0 cells (lacking mtDNA) after 48h arginine depletion by arginine deiminase (ADI).
(Submitter supplied) In this study, the effect of arginine deprivation on global gene expression in MDA-MB-231 and its ρ0 cells were examined. MDA-MB-231 ρ0 cells lack mitochondrial DNA and therefore have impaired OXPHOS function. Both parental and ρ0 cells were cultured in complete or arginine depleted medium for 48 hours. Comparative transcriptome analysis of both cell lines in complete growth medium versus arginine depleted medium were performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA408268
Series		Accession: GSE104105	ID: 200104105

1462. Gene expression profiles of isogenic single-cell derived clones of BRAF-mutated SK-MEL-5 melanoma cell lines
(Submitter supplied) We recently reported that single-cell derived isogenic subclones of SKMEL5 cells have differential initial sensitivity to BRAF-inhibitors. In order to probe differences among these subclones, we selected three subclones with unique drug responses: progressing (SK-MEL-5 SC10), stationary (SK-MEL-5 SC07), and regressing (SK-MEL-5 SC01) and performed RNASeq. This study examines differentially expressed genes (DEGs) among the subclones to identify the molecular basis for initial differences in drug sensitivity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA503257
Series		Accession: GSE122041	ID: 200122041

1463. Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL10558 11 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119759/
Series		Accession: GSE119759	ID: 200119759

1464. Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression [RNA-Seq]
(Submitter supplied) our study establishes FOXA1 as an important regulator of lineage plasticity mediated in part by TGF-β signaling and supports a novel therapeutic strategy to control lineage switching and potentially extend clinical response to antiandrogen therapies.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119757/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490188
Series		Accession: GSE119757	ID: 200119757

1465. Septin 9 over expression in MCF7
(Submitter supplied) Septin 9 (SEPT9), a member of the septin gene family, is strongly linked to cancer, particularly breast cancer, where genomic amplification occurs in ~11% of cases. SEPT9 is a putative oncogene as it is amplified in the form of double minute chromosomes in murine models of breast cancer, is a fusion partner of mixed lineage leukemia (MLL) gene in leukemia, and it is a known hot spot of retroviral tagging insertion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119449/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489270
Series		Accession: GSE119449	ID: 200119449

1466. N6-methyladenine DNA Modification in Glioblastoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 50 Samples
FTP download: GEO (BED, BIGWIG, BW, NARROWPEAK, TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118093/
Series		Accession: GSE118093	ID: 200118093

1467. RNA-seq Analysis of U87: Ctrl, U87:EGFR, U87:EGFRvIII, U87:EGFR+EGFRvIII and U87:EGFR+EGFRvIII KRAS KO
(Submitter supplied) We found that U87 cells expressing EGFR and EGFRvIII upregulated a large group of cytokines. The upregulation of many of these cytokines was dependent on KRAS.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117838/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483397
Series		Accession: GSE117838	ID: 200117838

1468. N6-methyladenine DNA Modification in Glioblastoma [RNA-seq]
(Submitter supplied) Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. While the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obsure. Here, we report the  identification of novel N(6)-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic regulation in human disease, the highly malignant brain cancer, glioblastoma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 11 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482757
Series		Accession: GSE117632	ID: 200117632

1469. Single-cell RNA-seq of melanoma ecosystems reveals sources of T cells exclusion linked to immunotherapy clinical outcomes
(Submitter supplied) Immune checkpoint inhibitors (ICI) produce durable responses in some melanoma patients, but many patients derive no clinical benefit, and the molecular underpinnings of such resistance remain elusive. Here, we leveraged single-cell RNA-seq (scRNA-seq) from 31 melanoma tumors and novel computational methods to interrogate malignant cell states that promote immune evasion. We identified a resistance program expressed by malignant cells that is associated with T cell exclusion and immune evasion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 7186 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115978/
Series		Accession: GSE115978	ID: 200115978

1470. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113229/
Series		Accession: GSE113229	ID: 200113229

1471. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [RNA-seq]
(Submitter supplied) We used a CRISPR-based screening approach to identify functional vulnerabilities in pediatric sarcoma cell types, identifying BRD9 as an important dependency in synovial sarcoma cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113227/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450466
Series		Accession: GSE113227	ID: 200113227

1472. RNA sequencing data for diffuse gastric cancer
(Submitter supplied) To identify altered transcriptomic profiles in early-onset diffuse gastric cancer (DGC), we performed RNA sequencing on DGCs collected from 80 young (≤ 45 years) Korean patients who had not been treated with chemotherapy or radiation
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 80 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110875/
Series		Accession: GSE110875	ID: 200110875

1473. Transcriptome analysis by RNA sequencing after treatment with JIB-04 in colorectal cancer
(Submitter supplied) We investigate RNA sequencing analysis revealed that the JIB-04 treatment altered the expression of genes that are involved in the cell cycle, apoptosis, and DNA replication and are also related to several cancers including colorectal cancer. JIB-04 also altered the expression of genes involved in various signaling pathways such as the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the Wnt signaling pathway, which is crucial for the proliferation and maintenance of colorectal cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416779
Series		Accession: GSE106407	ID: 200106407

1474. Hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes in choriocarcinoma cells
(Submitter supplied) We report the application of transcriptome sequencing for investigating of the hsa-miR-371a-5p and hsa-miR-518a-3p regulated genes. JAR, JEG-3 and BeWo choriocarcinoma cells were transfected with hsa-miR-371a-5p or hsa-miR-518a-3p inhibitors or control inhibitors. Totally, 237, 132 and 277 genes with > 2 folds change and adjusted P < 0.05 were upregulated in JAR, JEG-3 and BeWo cells respectively after hsa-miR-371a-5p knockdown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106394/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416704
Series		Accession: GSE106394	ID: 200106394

1475. RNA-seq analysis of THP-1 cell line upon knockdown of CHD4
(Submitter supplied) Epigenetic alterations contribute to leukemogenesis in childhood acute myeloid leukemia (AML). We used RNAi screens of AML cells together with non-transformed bone marrow cells and identified CHD4 as being required for AML maintenance. RNAi and CRISPR-Cas9 approaches, showed that CHD4 is essential for cell growth of leukemic cells in vitro, and disease progression in vivo, including primary childhood AML cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416703
Series		Accession: GSE106392	ID: 200106392

1476. Gene expression profiling study by RNA-seq in PDX model based diffuse type gastric cancers.
(Submitter supplied) We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out RNA-seq based transcriptome profiling using 15 stomach samples including three PDX lines (HGC-3, HGC-8, and HGC-20) and normal-looking surrounding tissues. Via comparative analysis between cells and tissues, we identified significant gene set associated with each cell and observed that genes involved in AKT signalling pathway were commonly associated with all PDX lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416330
Series		Accession: GSE106338	ID: 200106338

1477. 3'-seq and RNA-seq of APA modulator_U2OS
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 32 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99527/
Series		Accession: GSE99527	ID: 200099527

1478. APA modulator_U2OS_RNA-seq
(Submitter supplied) RNA-seq data treated with small molecule compounds that modulate alternative polyadenylation
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388702
Series		Accession: GSE99526	ID: 200099526

1479. USP7 controls the oncogenic transcriptional circuitry and is a novel therapeutic target in T cell leukemia
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling. In this study we chemically inhibited the deubiquinating enzyme USP7 and assayed for gene expression changes. This piece of data was further integrated to epigenetic changes using ChIP-Sequencing analysis of H3K27me3, H2AUb, H2BUb, H3K27Ac and H3K79me2 upon inhibition of USP7. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 71 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97435/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381790
Series		Accession: GSE97435	ID: 200097435

1480. Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells
(Submitter supplied) Long RNA-seq analysis on cellular and extracellular samples from a KRAS mutant colorectal cancer cell model, in association with Hinger et al 2018
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121964/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA501808
Series		Accession: GSE121964	ID: 200121964

1481. Identification of Sin3B regulated genes during quiescence
(Submitter supplied) We report differences in gene expression between WT and Sin3B KO T98G cells throughout the cell cycle
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498664
Series		Accession: GSE121857	ID: 200121857

1482. CHD7 is Suppressed in the Perinecrotic/Ischemic Microenvironment and is a Novel Regulator of Angiogenesis
(Submitter supplied) In a study focused on the role for CHD7 in angiogenesis we completed RNA-sequencing of D456, a glioblastoma xenograft line and neural precursor cells after CHD7 knockdown
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489973
Series		Accession: GSE119688	ID: 200119688

1483. Reciprocal Reprogramming of Cancer Cells and Associated Mesenchymal Stem Cells in Gastric Cancer.
(Submitter supplied) We utilized gastric cancer cells (GSC1) to demonstrate subversion of naïve Mesenchymal Stem Cells (MSC) from adjacent tissue, which are reprogrammed to express a tumor-promoting phenotype, whose cardinal manifestation is to sustain cancer stem cells. Paracrine effects of such primed MSC are sufficient to enable 2D growth of GSC1, while cell-cell interactions are necessary for 3D growth or in vivo tumor formation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111556/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437396
Series		Accession: GSE111556	ID: 200111556

1484. A facile method for generating tumorigenic cancer stem cell spheroids from diverse cancer cell lines
(Submitter supplied) Although cancer stem cells (CSCs) are thought to be responsible for tumor recurrence and resistance to chemotherapy, CSC-related research and drug development have been hampered by the limited supply of patient-derived diverse CSCs. Here, we developed a functional polymer thin film (PTF) platform that promotes conversion of human cancer cell lines to highly tumorigenic spheroids without the use of biochemical or genetic manipulations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106848/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418170
Series		Accession: GSE106848	ID: 200106848

1485. Expression analysis of THP1 cells following shRNA knock-down of RUVBL2
(Submitter supplied) We used an inducible shRNA system and RNA-Seq to examine gene expression changes in acute myeloid leukemia THP1 cells following silencing of RUVBL2. RUVBL2 is a AAA+ ATPase that functions in a number of cellular processes, including chromatin remodeling and trnascriptional control, and is critical for survival of acute myeloid leukemia cells and in vivo disease progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415069
Series		Accession: GSE105253	ID: 200105253

1486. Genomic basis for clinical response to histone deacetylase inhibition in advanced urothelial carcinoma
(Submitter supplied) Abstract  Background: Histone deacetylase (HDAC) inhibition has shown some efficacy in urothelial carcinoma (UC); the genomic basis for clinical response is not known.  Methods: In two separate phase I clinical trials testing HDAC inhibitors in advanced solid tumors, we identified one patient with advanced UC who had a complete response (CR) to belinostat and one with advanced UC who had a partial response (PR) to panobinostat. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407632
Series		Accession: GSE103928	ID: 200103928

1487. Transcriptome analysis of Group 3 and 4 medulloblastoma orthotopic xenograft mice with digoxin treatment
(Submitter supplied) RNA-seq data of Group 3 and 4 medulloblastoma with digoxin treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115542/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475298
Series		Accession: GSE115542	ID: 200115542

1488. Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of FOXD3 antisense RNA 1 (FOXD3-AS1)
(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of publically available microarray datasets, we discovered a novel 963-bp lncRNA, named FOXD3 antisense RNA 1 (FOXD3-AS1), as an independent prognostic marker for favorable clinical outcome of NB patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414427
Series		Accession: GSE105016	ID: 200105016

1489. Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1)
(Submitter supplied) Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of a public microarray dataset and rapid amplification of cDNA ends, we identified v-ets erythroblastosis virus E26 oncogene homolog 1 (Ets-1) promoter-associated noncoding RNA (pancEts-1) as a novel lncRNA associated with the progression of NB. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104950/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414220
Series		Accession: GSE104950	ID: 200104950

1490. Arrayed molecular barcoding identifies TNFSF13 as a positive regulator of acute myeloid leukemia-initiating cells
(Submitter supplied) Dysregulation of cytokines in the bone marrow microenvironment promotes acute myeloid leukemia cell growth. Due to the complexity and low throughput of in vivo stem-cell based assays, studying the role of cytokines in the bone marrow niche in a screening setting is challenging. Herein, we developed an ex vivo cytokine screen using 11 arrayed molecular barcodes, allowing for a competitive in vivo readout of leukemia-initiating capacity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104425/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412591
Series		Accession: GSE104425	ID: 200104425

1491. Identification of global XBP1s target gene expression in human prostate cancer cells
(Submitter supplied) To gain insight into the global XBP1s target gene profile in prostate cancer cells, we performed RNA-seq analysis in LNCaP cells upon either XBP1 siRNA-mediated knockdown (siXBP1) or MKC8866-mediated IRE1α inhibition.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103864/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407349
Series		Accession: GSE103864	ID: 200103864

1492. MKL1 augments megakaryocyte maturation by enhancing the SRF regulatory axis [RNA-seq]
(Submitter supplied) SRF is a ubiquitous transcription factor that binds DNA in association with myocardin-family proteins (e.g. MKL1), or the ternary complex factor (TCF) family of ETS proteins. In primary hematopoietic cells, knockout of either SRF or MKL1 decreases megakaryocyte maturation caused thrombocytopenia, and MKL1 over-expression (MKL1OE) in the Human Erythroleukemia (HEL) cell line enhances megakaryopoiesis, but the mechanisms underlying these effects are unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445458
Series		Accession: GSE112277	ID: 200112277

1493. Transcriptome analysis of total RNA in human osteosarcoma cell line U2OS before and after inhibition of zinc finger protein ZNF768
(Submitter supplied) Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen.  After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer’s protocol. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111881/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438476
Series		Accession: GSE111881	ID: 200111881

1494. Lineage tracking reveals dynamic relationships of T cells in colorectal cancer
(Submitter supplied) T cells are central players in cancer immunotherapy1, yet some of their fundamental properties such as development and migration within tumours remain elusive. The enormous T cell receptor (TCR) repertoire, required for recognising foreign and self-antigens2,3, could serve as lineage tags to track these T cells in tumours4. Here, we obtained transcriptomes of 11,138 single T cells from 12 colorectal cancer (CRC) patients and developed STARTRAC (Single T-cell Analysis by Rna-seq and Tcr TRACking) indices to quantitatively analyse dynamic relationships among 20 identified T cell subsets with distinct functions and clonalities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108989/
Series		Accession: GSE108989	ID: 200108989

1495. LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 35 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116818/
Series		Accession: GSE116818	ID: 200116818

1496. LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state [human]
(Submitter supplied) Deregulated activity of the LATS tumor suppressors has broad implications on cellular and tissue homeostasis. We examined the consequences of downregulation of either LATS1 or LATS2 in breast cancer. Consistent with their proposed tumor suppressive roles, expression of both paralogs is significantly downregulated in human breast cancer, and loss of either paralog accelerated mammary tumorigenesis in mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480289
Series		Accession: GSE116816	ID: 200116816

1497. Identifying novel small RNA biomarkers unique to patients with gastric cancer
(Submitter supplied) Extracellular RNA (exRNA) is an emerging paradigm as endocrine signals in cellular communication, biomarker development, therapeutic applications and systemic physiology. This project is to test the hypothesis that salivary extracellular RNA (exRNA) can be developed for the clinical detection of human diseases. Our laboratory first reported the existence of a transcriptome and microRNA profile in cell free saliva followed by its scientific characterizations and clinical utilities including biomarker development for molecular oncology applications. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 198 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121870/
Series		Accession: GSE121870	ID: 200121870

1498. Induced MIST1 and PTF1a Expression in Pancreatic Ductal Adenocarcinoma Cells
(Submitter supplied) Purpose: The goal of the study was to determine the effects of forced expression of the acinar transcription factors MIST1 and PTF1a in PDAC cells. Methods: Doxycycline inducible MIST1myc and PTF1amyc Panc-1 cells were generated using Clontech's Tetone System and subjected to RNA-Sequencing following doxycycline treatment. Results: 50 million sequence reads were mapped to the human genome. Data suggests acinar associated molecules were induced upon doxycyline treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106290/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416132
Series		Accession: GSE106290	ID: 200106290

1499. Whole transcriptomic sequencing of CD133+CD44+ cancer stem cells from laryngeal squamous carcinoma cell line
(Submitter supplied) To understand the gene expression profiling of cancer stem cells of laryngeal squamous carcinoma, the total RNA of CD133+CD44+ laryngeal cancer stem cells (isolated from LSCC cell line TU-177, named TDP), CD133-CD44- cells (TDN) and parental TU-177 (unsorted TU-177 cells, named TPT) was extracted, followed by RNA sequencing. Differentially expression of lncRNA, mRNA, and circRNA was identified.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106283/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416118
Series		Accession: GSE106283	ID: 200106283

1500. Linking single-cell measurements of mass, growth rate, and gene expression
(Submitter supplied) We introduce a microfluidic platform that enables single-cell mass and growth rate measurements upstream of single-cell RNA-sequencing (scRNA-seq) to generate paired single-cell biophysical and transcriptional data sets. Biophysical measurements are collected with a serial suspended microchannel resonator platform (sSMR) that utilizes automated fluidic state switching to load individual cells at fixed intervals, achieving a throughput of 120 cells per hour. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL19057 762 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121655/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA498045
Series		Accession: GSE121655	ID: 200121655

1501. A transcription factor addiction imposed by an oncogene promoter sequence
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 83 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115238/
Series		Accession: GSE115238	ID: 200115238

1502. A transcription factor addiction imposed by an oncogene promoter sequence [RNA-seq]
(Submitter supplied) Transcriptome analysis by high throughput sequencing
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 63 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474224
Series		Accession: GSE115237	ID: 200115237

1503. Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy
(Submitter supplied) The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. more...
Organism:	Drosophila melanogaster; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL19132 111 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112608/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448451
Series		Accession: GSE112608	ID: 200112608

1504. RNA-seq of YB5 cells treated with HH1
(Submitter supplied) RNA-seq was performed after YB5 cells were treated with DAC,  HH1 or the combination of the two. RNA-seq was also perfomed after viral transduction using a TET-off dnCDK9 construct
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104837/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413957
Series		Accession: GSE104837	ID: 200104837

1505. Next Generation Sequencing Analysis of control and hnRNPK-/- RKO cells Transcriptomes
(Submitter supplied) We generated the hnRNPK-/- RKO cells,and collected the cells at 2 days after transfectd with siRNA. Then,we extracted RNAs and performed next generation sequencing. By comparing sequcing data from control and hnRNPK -/- samples, we profiled the alternative splicing events and gene expression regulated by hnRNPK in CRC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85522/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338737
Series		Accession: GSE85522	ID: 200085522

1506. Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1-dependent gene expression by Epstein-Barr virus latent membrane protein 1
(Submitter supplied) Latent membrane protein 1 (LMP1) is the major transforming protein of Epstein-Barr virus (EBV) and is critical for EBV-induced B-cell transformation in vitro. Poly(ADP-ribose) polymerase 1 (PARP1) regulates accessibility of chromatin, alters functions of transcriptional activators and repressors, and has been directly implicated in transcriptional activation. Previously we showed that LMP1 activates PARP1 and increases Poly(ADP-ribos)ylation (PARylation) through PARP1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497437
Series		Accession: GSE121476	ID: 200121476

1507. GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis
(Submitter supplied) Background: Amyotrophic lateral sclerosis (ALS) is currently an incurable disease without highly effective pharmacological treatments. The peptide drug GM604 (GM6) was developed as a candidate ALS therapy, which has demonstrated safety and encouraging outcomes in a phase II clinical trial. GM6 is hypothesized to bolster neuron survival through regulation of developmental pathways, but mechanisms of action are not fully understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471631
Series		Accession: GSE114510	ID: 200114510

1508. Effect of SETD1A knockdown on global gene expression in MCF-7 cells
(Submitter supplied) SETD1A is a histone H3K4 methyltransferase and function as a coactivator for nuclear receptors (NRs) and other transcription factors. We performed genome-wide gene expression analysis in non-specific siRNA transfected or SETD1A knockdown MCF-7 cells to investigate global gene expression changes induced by SETD1A knockdown.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395717
Series		Accession: GSE101860	ID: 200101860

1509. Gene expression profiling U87 cells knocking down Glud1 under low glucose treatment
(Submitter supplied) U87 cells (shGlud1 and shNT) were treated with low glucose for 6 hours, then mRNA were extracted for high-throughput sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121580/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497832
Series		Accession: GSE121580	ID: 200121580

1510. Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies
(Submitter supplied) Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121553/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497782
Series		Accession: GSE121553	ID: 200121553

1511. A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of advanced human retinoblastoma
(Submitter supplied) Persistent or recurrent retinoblastoma (RB) is associated with the presence of vitreous or/and subretinal seeds in advanced RB and represents a major cause of therapeutic failure. This necessitates the development of novel therapies and thus requires a model of advanced RB for testing candidate therapeutics. To this aim, we established and characterized a three-dimensional, self-organizing organoid model derived from chemotherapy-naïve tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL24676 3 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120710/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494224
Series		Accession: GSE120710	ID: 200120710

1512. Transcriptomic analysis of T84 colon carcinoma cell line treated with trametinib, JQ1 or their combination
(Submitter supplied) T84 cells were treated with DMSO, 30nM trametinib (MEKi), 1µM JQ1 (BRD4i) or the combination of trametinib and JQ1 (combo) for 24h.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118548/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486000
Series		Accession: GSE118548	ID: 200118548

1513. Transcriptomic analysis of trametinib-resistant HCT116 colorectal carcinoma cells compared to the parental control cells
(Submitter supplied) HCT116 cells were treated with with increasing concentrations of trametinib over 2 months. Drug-resistant clones emerged and were cultured in the presence of 30 nmol/L trametinib. These cells exhibited a greater than 10-fold increase in the GI50 for trametinib compared to the parental cell line. RNA-seq of the resistant clone HCT116_R4 versus the parental cells identified differentially expressed genes potentially involved in resistance.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118490/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485782
Series		Accession: GSE118490	ID: 200118490

1514. SMAD2 binding regions in breast cancer cell line and RNA-seq transcriptome analyses in T47D
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL17303 15 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117502/
Series		Accession: GSE117502	ID: 200117502

1515. RNA-seq transcriptome analyses in T47D cells treated with ActA and Palbociclib.
(Submitter supplied) We performed SMAD2 ChIP-seq analysis in T47D cells with/without Palbociclib treatment. To validate whether the changes in SMAD2 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analyses in T47D with/without ActA stimulation and Palbo treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (BW, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117497/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482345
Series		Accession: GSE117497	ID: 200117497

1516. SHQ1 regulation of RNA splicing is required for T-lymphoblastic leukemia cell survival
(Submitter supplied) T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with complicated heterogeneity. Although expression profiling reveals common elevated genes in distinct T-ALL subtypes, little is known about their functional role(s) and regulatory mechanism(s). We here show the expression of SHQ1, an H/ACA snoRNPs assembly factor involved in snRNA pseudouridylation, is specifically and highly expressed in T-ALL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117264/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481581
Series		Accession: GSE117264	ID: 200117264

1517. Analysis of KMT2D Knockdown/Control PC-3 Cell Line
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL23227 5 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94817/
Series		Accession: GSE94817	ID: 200094817

1518. Next Generation Sequencing Facilitates Quantitative Analysis of KMT2D Knockdown/Control PC-3 Cell Line Transcriptomes
(Submitter supplied) KMT2D is a histone methyltransferase for catalyzing the monomethylation of H3K4. Previous studies have indentified that H3K4me1 is prominent on active enhancers and participates in gene expression regulation. To further examine the transcriptional changes in response to KMT2D depletion, we performed RNA-seq with KMT2D knockdown and control PC-3 cells by BGISEQ-500
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94807/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374489
Series		Accession: GSE94807	ID: 200094807

1519. Transcriptomics analysis of gene expression in multiple human and mouse cells and tissues
(Submitter supplied) RNA was isolated from siCTRL, siNSUN2 HeLa or 3T3-L1 cells, human cells (embryonic kidney T cell line 293T; colon cancer cell line HCT116; hepatocellular carcinoma cell line Huh7; embryonic lung fibroblast cell line MRC-5; glioma cell line SNB19), mouse cells (kidney collecting duct cell line M-1; cervical cancer cell line U14) and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21493 GPL11154 GPL13112 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74333/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301440
Series		Accession: GSE74333	ID: 200074333

1520. Chemical Modulation of Glycolysis Regulates the KEAP1-NRF2 Pathway Through a Metabolite-Induced Posttranslational Modification
(Submitter supplied) Glycolysis is a master regulator of cellular energy, synthesis and redox regulation, however the mechanisms that underlie the responses to and regulation of changing glucose metabolism are incompletely understood. The NRF2-antioxidant response element (ARE) pathway serves as a central regulator of cellular stress by sensing and eliminating 2 chemically reactive species in the cell. A phenotypic high-throughput chemical screen for novel activators of NRF2 signaling identified an inhibitor of the glycolytic enzyme PGK1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116642/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479768
Series		Accession: GSE116642	ID: 200116642

1521. Global transcriptional profiling changes upon knockdown of G9a in human non-small cell lung cancer cells
(Submitter supplied) The experiment was designed to display differential gene expression profiling changes in two human Non-small cell lung cancer cells upon knockdown of G9a/EHMT2, by using RNAseq technology.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451303
Series		Accession: GSE113493	ID: 200113493

1522. Differentiation enhances Zika virus infection in neuronal brain cells
(Submitter supplied) Zika virus (ZIKV) is an emerging, mosquito-borne pathogen associated with a widespread 2015–2016 epidemic in the Western Hemisphere and a proven cause of microcephaly and other fetal brain defects in infants born to infected mothers. ZIKV infections have been also linked to other neurological illnesses in infected adults and children, including Guillain-Barré syndrome (GBS), acute flaccid paralysis (AFP) and meningoencephalitis, but the viral pathophysiology behind those conditions remains poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497590
Series		Accession: GSE121534	ID: 200121534

1523. Comparison of expression profiles of APP-depleted prostate cancer cells (LNCaP)
(Submitter supplied) This analysis determines the relevanve of APP in prostate cancer as potential novel redox-regulator in androgen-responsive and castration-refractory prostate cancer
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98009/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383657
Series		Accession: GSE98009	ID: 200098009

1524. Expression profiles in circRHOT1-deficient or control HCC cells.
(Submitter supplied) RNA-sequencing of Human hepatocellular carcinoma (HCC) cells We analyzed two circRNA profiles expressed in human HCC tissues and identified circRHOT1 as a conserved and dramatically upregulated circRNA in HCC tissues. HCC patients displaying high circRHOT1 level possessed poor prognosis. We demonstrated circRHOT1 significantly promoted HCC growth and metastasis. In order to investigate the mechansim of circRHOT1, we constructed circRHOT1-deficient HCC cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121468/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496386
Series		Accession: GSE121468	ID: 200121468

1525. Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to ER-directed therapies
(Submitter supplied) Estrogen receptor positive (ER+) breast cancers that develop resistance to therapies that target the ER are the most common cause of breast cancer death. Beyond mutations in ER, which occur in 25-30% of patients treated with aromatase inhibitors (AIs), our understanding of clinical mechanisms of resistance to ER-directed therapies remains incomplete. We identified activating HER2 mutations in metastatic biopsies from eight patients with ER+ metastatic breast cancer who had developed resistance to ER-directed agents, including AIs, tamoxifen, and fulvestrant. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 864 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121411/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497449
Series		Accession: GSE121411	ID: 200121411

1526. RNA-Seq of osteosarcoma cell lines
(Submitter supplied) The Alternative Lengthening of Telomeres (ALT) pathway stimulates telomere elongation and prevents cellular senescence in approximately 60% of osteosarcoma.  While the precise mechanisms underlying the ALT pathway are unclear, mutations in the chromatin remodeling protein ATRX, histone chaperone DAXX, and the histone variant H3.3, correlate with ALT status. ATRX and DAXX facilitate deposition of the histone variant H3.3 within heterochromatic regions including the telomere suggesting that loss of ATRX, DAXX, and/or H3.3 lead to defects in heterochromatin maintenance at telomeres, ultimately contributing to ALT activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 39 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118488/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485781
Series		Accession: GSE118488	ID: 200118488

1527. Heterogeneity of Androgen Receptor Splice Variant-7 (AR-V7) Protein Expression and Response to Therapy in Castration Resistant Prostate Cancer (CRPC)
(Submitter supplied) Liquid biopsies have demonstrated that the constitutively active androgen receptor splice variant-7 (AR-V7) associates with reduced response and overall survival (OS) from endocrine therapies in castration resistant prostate cancer (CRPC). However, these studies provide little information pertaining to AR-V7 biology and expression in prostate cancer (PC) tissue. Following generation and validation of a novel AR-V7 antibody for immunohistochemistry (IHC); nuclear AR-V7 protein expression was determined for 358 primary prostate samples (358 patients) and 293 metastatic biopsies (194 patients). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 41 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118435/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485585
Series		Accession: GSE118435	ID: 200118435

1528. Antioxidant metabolism in activated CD8+ T cells regulates stem-like human memory T cell formation and anti-tumor immunity
(Submitter supplied) Adoptive T cell transfer (ACT) immunotherapy benefits from early-differentiated memory stem-like T (TSCM) cells capable to persist in the long term and to generate potent anti-tumor effectors. Due to their paucity ex vivo, TSCM can be derived from less differentiated naïve precursors but the molecular signals at the basis of their generation are ill-defined. We found that less differentiated human circulating CD8+ T cells display substantial antioxidant capacity ex vivo compared to more differentiated central and effector memory T cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114765/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472586
Series		Accession: GSE114765	ID: 200114765

1529. HP1γ is required for G9a/GLP coactivator function with the glucocorticoid receptor in Nalm6 cells
(Submitter supplied) Using a genome-wide analysis, we demonstrated that HP1γ is selectively required for GC-regulated expression of GR target genes that require G9a and GLP, consistent with our previous finding that automethylated G9a and GLP recruit HP1g to specific genomic GR binding sites.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483191
Series		Accession: GSE117796	ID: 200117796

1530. Non-coding regions are the main source of tumor-specific antigens
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL19057 GPL13112 GPL11154 15 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113992/
Series		Accession: GSE113992	ID: 200113992

1531. Non-coding regions are the main source of tumor-specific antigens [human]
(Submitter supplied) Purpose: Tumor-specific antigens (TSAs) represent ideal targets for cancer immunotherapy, but very few of them have been identified. Therefore, the goal of this study was to develop a novel approach, combining RNA-Sequencing and mass spectrometry, to enlarge the landscape of actionable TSAs in seven human primary samples, namely 4 B-ALL and 3 lung tumor biopsies. Methods: We performed RNA-Sequencing on each primary tumor sample (unreplicated) with the Illumina HiSeq2000. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 7 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113972/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454710
Series		Accession: GSE113972	ID: 200113972

1532. Mechanosensitive ion channel regulates tissue stiffening to promote glioma aggression
(Submitter supplied) Tissue stiffening is a physical hallmark of solid tumor. In our study, we found that the mechanosensitive ion channel PIEZO1 can be tumor cells force sensor and transducer that regulate the altered tissue mechanics. We examined the transcriptional changes modulated by depletion of PIEZO1 in two human GBM cell lines. We found that with PIEZO1 KD, the components involved in ECM organization, focal adhesion formation, cytoskeleton, and mitosis, which contribute to tissue stiffness, are down-regulated.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450606
Series		Accession: GSE113261	ID: 200113261

1533. Identification of target genes regulated by NANOG-HDAC1 axis
(Submitter supplied) To gain insight into the role of HDAC1 in NANOG-mediated transcriptional regulation, we performed genome-wide RNA-sequencing analysis (RNA-seq) in CaSki-no insert-siGFP, CaSki-NANOG-siGFP and CaSki-NANOG-siHDAC1 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88965/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349253
Series		Accession: GSE88965	ID: 200088965

1534. A non-canonical GLTSCR1L-containing BAF complex mediates H3K27ac-dependent enhancer activities
(Submitter supplied) H3K27ac is known to associate with regulatory active enhancers, but it’s exact role in enhancer function remains elusive. Using mass spectrometry-based interaction proteomics, we identified the Super Elongation Complex (SEC) and GBAF, a non-canonical GLTSCR1L- and BRD9-containing SWI/SNF chromatin remodeling complex, to be major interactors of H3K27ac. Our interaction proteomics analysis refined the composition of GBAF by adding BCL7A/B/C as a new subunit. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL11154 GPL18573 38 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121351/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA497106
Series		Accession: GSE121351	ID: 200121351

1535. RNA seq data of Hep3B-control, Hep3B-sertraline, Hep3B-XL413, Hep3B-XL413-sertraline, Huh7-control, Huh7-sertraline, Huh7-XL413, Huh7-XL413-sertraline cells
(Submitter supplied) Hep3B and Huh7 cells pre-treated with XL413 for 10 days to induce senescence prior to sertraline treatment for 24 hours. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496576
Series		Accession: GSE121277	ID: 200121277

1536. CDC7 inhibition induces a senescence-like state in Hep3B and Huh7 cells
(Submitter supplied) Purpose: to check senescence gene expression signature in XL413 treated liver cancer cells. Methods: Hep3B and Huh7 cells are treated with XL413 for 4 days. For RNA sequencing, the library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). Gene set enrichment analysis was performed using gene set enrichment analysis software. The FRIDMAN_SENESCENCE_UP gene set was used to assess the enrichment of senescence-associated genes in the XL413-treated versus control cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121276/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496577
Series		Accession: GSE121276	ID: 200121276

1537. Transciptomic profiling of human fetal lung samples
(Submitter supplied) Fibroblast Growth Factor (FGF) signaling plays an important role in lung organogenesis. Over recent decades, FGF signaling in lung development has been extensively studied in animal models. However, little is known about the expression, localization and functional roles of FGF ligands during human fetal lung development. Therefore, we aimed to determine the expression and function of several FGF ligands and receptors in human lung development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL20301 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121238/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA496465
Series		Accession: GSE121238	ID: 200121238

1538. CALGB 40601: Randomized Phase III Trial of Paclitaxel Combined With Trastuzumab, Lapatinib, or Both As Neoadjuvant Treatment of HER2-Positive Primary Breast Cancer
(Submitter supplied) CALGB 40601 was activated as a 3-arm study (paclitaxel + trastuzumab + lapatinib [THL], paclitaxel + trastuzumab [TH] and paclitaxel + lapatinib [TL]). In December 2010, twoneoadjuvant studies were presented at the Cancer Therapy and Research Center-American Association for Cancer Research (CTRC-AACR) San Antonio Breast Cancer Symposium that affected the scientific and practical enthusiasm for the TL arm. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 265 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116335/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448797
Series		Accession: GSE116335	ID: 200116335

1539. Profiling in vivo Bone Lesion (IVBL) and Orthotopic tumors by Next Generation Sequencing
(Submitter supplied) Based on RNA-seq, we performed transcriptomic profiling to examine the differences between Orthotopic and IVBL (in vivo bone lesion). We found Calcium signalling is upregulated in IVBL and correlated to the expression of gap junctions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (RDATA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433732
Series		Accession: GSE110451	ID: 200110451

1540. RNA-seq analysis of BAP1-depleted uveal melanoma cells
(Submitter supplied) OCM-1A uveal melanoma cells were infected with lentivirus carrying shRNA expression constructs specific for BAP1 or GFP (control), and placed under selection for 6 days. RNA-seq was performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110193/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433106
Series		Accession: GSE110193	ID: 200110193

1541. Three-component mixed cell lines RNA-seq experiment
(Submitter supplied) To generate this dataset in RNA-seq, we performed a mixing experiment, in which we mixed mRNAs from three cell lines: lung adenocarcinoma in humans (H1092), cancer-associated fibroblasts (CAFs) and tumor infiltrating lymphocytes (TIL), at different proportions to generate 32 samples, including 9 samples that correspond to three repeats of a pure cell line sample for three cell lines. The RNA amount of each tissue in the mixture samples was calculated on the basis of real RNA concentrations tested in the biologist’s lab. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495812
Series		Accession: GSE121127	ID: 200121127

1542. SHP2 Drives Adaptive Resistance to ERK Signaling Inhibition in Molecularly Defined Subsets of ERK-dependent Tumors
(Submitter supplied) We performed RNA sequencing analysis using NextSeq500 to identify drivers that mediate feedback RAS activation in BRAF(V600E) cells that are SHP2 independent.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121117/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495756
Series		Accession: GSE121117	ID: 200121117

1543. Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells
(Submitter supplied) Background: Breast cancer stem cells (BCSCs) are considered responsible for cancer relapse and drug-resistance. Understanding the identity of BCSCs may open new avenues in breast cancer therapy. Although several discoveries have been made on BCSCs characterization, the factors critical to BCSCs is largely unclear. This study was aimed to determine whether genomic mutation contributes to the acquisition of cancer stem-like phenotype, and to investigate the genetic and transcriptional features of BCSCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116180/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477551
Series		Accession: GSE116180	ID: 200116180

1544. mRNA-seq in MCF7 cells in response to 4-hydroxytamoxifen (OHT)
(Submitter supplied) Purpose: Study the temporal effect of OHT on gene expression in MCF7 cells using mRNA-seq. Methods: MCF7 cells were treated with 100nM OHT for 2h, 6h and 24h or 24h with vehicle alone (ethanol). Six biological replicates of each time point were included in the analysis. For the library preparation the Illumina TruSeq Stranded mRNA Library Prep Kit High Throughput was used and 2 lanes of SE50 were run on HiSeq 4000. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414078
Series		Accession: GSE104872	ID: 200104872

1545. Stable knockdown of PLAGL2 in hepatocellular carcinoma cells
(Submitter supplied) Pleomorphic adenoma gene like-2 (PLAGL2), along with PLAG1 and PLAGL1, belong to PLAGL gene family of zinc-finger transcription factors, PLAG proteins are highly homologous, and with the structures of the seven C2H2 zinc finger domain on the N-terminal. PLAG proteins recognize similar GC rich consensus DNA-binding sequences, that these family members function as regulators of transcription target genes and pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495569
Series		Accession: GSE121072	ID: 200121072

1546. RIG-I and MDA5 fRIP during KSHV lytic reactivation
(Submitter supplied) The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as restriction factors for RNA viruses. However, evidence suggests RLRs participate in innate immune recognition of other pathogens, including DNA viruses. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human gammaherpesvirus and the etiological agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL21290 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116650/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479810
Series		Accession: GSE116650	ID: 200116650

1547. Identification of Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer
(Submitter supplied) Background: Patients with locally advanced or recurrent prostate cancer typically undergo androgen deprivation therapy (ADT), but the benefits are often short-lived, and responses are variable. ADT failure results in castration-resistant prostate cancer (CRPC), that inevitably leads to metastasis. We hypothesized that differences in tumor transcriptional programs may reflect differential responses to ADT and subsequent metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111177/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436129
Series		Accession: GSE111177	ID: 200111177

1548. Epigenetic reprogramming of melanoma cells by vitamin C treatment
(Submitter supplied) In this study we show that ascorbate (vitamin C) shifts the  transcriptome of melanoma cells, and decreases malignant phenotypes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495630
Series		Accession: GSE121095	ID: 200121095

1549. Vitamin C Promotes Apoptosis in Breast Cancer Cells by Increasing TRAIL Expression
(Submitter supplied) In this study we show that ascorbate (vitamin C) shifts the transcriptome of MDA-MB-231 cells and increases apoptosis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121093/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495625
Series		Accession: GSE121093	ID: 200121093

1550. Deciphering clonal evolution and dissemination of Multiple Myeloma cells in vivo
(Submitter supplied) Clonal evolution drives tumor progression, dissemination and relapse in cancer, and dissemination or metastasis of the tumor cells from primary site to other organs is the leading cause of death for cancer patients. This multi-stage process requires tumor cells to survive in the circulation, extravasate at distant sites, then colonization. The whole process involves contributions from both the tumor cells and microenvironment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA495356
Series		Accession: GSE121007	ID: 200121007

1551. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 24 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116136/
Series		Accession: GSE116136	ID: 200116136

1552. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner [Huh-7]
(Submitter supplied) The oncofetal mRNA-binding protein IGF2BP1 and the transcriptional regulator SRF modulate gene expression in cancer. In cancer cells, we demonstrate that IGF2BP1 promotes the expression of SRF in a conserved and N6-methyladenosine (m6A) dependent manner by impairing the miRNA-directed decay of the SRF mRNA. This results in enhanced SRF-dependent transcriptional activity and promotes tumor cell growth and invasion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116133/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477360
Series		Accession: GSE116133	ID: 200116133

1553. IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner [ES-2]
(Submitter supplied) The oncofetal mRNA-binding protein IGF2BP1 and the transcriptional regulator SRF modulate gene expression in cancer. In cancer cells, we demonstrate that IGF2BP1 promotes the expression of SRF in a conserved and N6-methyladenosine (m6A) dependent manner by impairing the miRNA-directed decay of the SRF mRNA. This results in enhanced SRF-dependent transcriptional activity and promotes tumor cell growth and invasion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116059/
Series		Accession: GSE116059	ID: 200116059

1554. YAP and MRTF-A, transcriptional co-activators of RhoA- mediated gene expression, are critical for glioblastoma tumorigenicity
(Submitter supplied) The role of YAP (Yes associated protein 1 gene) and MRTF-A (Megakaryoblastic Leukemia gene, MLK1), two transcriptional co-activators regulated downstream of GPCRs (G-protein coupled receptor) and RhoA, in growth of glioblastoma cells and in vivo GBM tumor development was explored using human glioblastoma cell lines  (1321N1) and tumor initiating cells derived from patient derived xenografts (PDX)PDX (GSC-23) cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111571/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437452
Series		Accession: GSE111571	ID: 200111571

1555. Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients
(Submitter supplied) We investigated the expression profiles in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 132 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413744
Series		Accession: GSE104744	ID: 200104744

1556. HiSeq analysis of human gene expression profile following infection with highly pathogenic avian influenza A virus (H5N1; A/Chicken/Vietnam/0008/04)
(Submitter supplied) Current prophylactic and therapeutic strategies targeting human influenza viruses include vaccines and antivirals. Given variable rates of vaccine efficacy and antiviral resistance, alternative strategies are urgently required to improve disease outcomes. Here we describe the use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar epithelial type II (ATII) cells infected with highly pathogenic avian influenza H5N1 virus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119767/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490197
Series		Accession: GSE119767	ID: 200119767

1557. Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution
(Submitter supplied) High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other
Platform: GPL16791 18 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA439006
Series		Accession: GSE112048	ID: 200112048

1558. Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 68 Samples
FTP download: GEO (H5, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111462/
Series		Accession: GSE111462	ID: 200111462

1559. Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [mini_dropseq]
(Submitter supplied) Studying dynamic transcripts in single cells (SC) requires large numbers of timed samples. We report an easy to use protocol to stabilize RNA in intact SCs without perturbing transcriptional patterns, and demonstrate its applicability for SC transcriptome assays with cells and tissue. We identify a gene-specific hierarchical pattern of all-or-none transcript induction elicited by different concentrations of pulsatile hormone stimuli in pituitary gonadotropes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111458/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437107
Series		Accession: GSE111458	ID: 200111458

1560. Pomalidomide inhibits PD-L1 induction to promote anti-tumor immunity
(Submitter supplied) We examined genome-wide how pomalidomide affects IFN-gamma-induced PD-L1 expression in human melanoma cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494725
Series		Accession: GSE120844	ID: 200120844

1561. MYC interacts with the G9a histone methyltransferase to drive transcriptional repression and tumorigenesis
(Submitter supplied) MYC is an oncogenic driver that regulates transcriptional activation and repression, yet molecular mechanisms of MYC transformation remain unclear. We demonstrate that MYC interacts with the G9a H3K9-methyltransferase complex to control transcriptional repression. Inhibiting G9a hinders MYC chromatin binding at MYC-repressed genes and de-represses gene expression to antagonize cellular transformation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115024/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473533
Series		Accession: GSE115024	ID: 200115024

1562. Mapping multi-layered regulation in response to environmental stress
(Submitter supplied) We have mapped transcript and protein concentrations in cervical cancer cells responding to treatment with tunicamycin over an eight hour time course. We complement this dataset with RNA footprints of ribosomes and non-ribosomal proteins to determine changes in translation and trans-factor binding. The goals of this study are to unveil the time dependent complexity of the signaling pathways at the level of transcription and  translation during different stress conditions like stress of the endoplasmic reticulum and oxidative stress.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113171/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450369
Series		Accession: GSE113171	ID: 200113171

1563. A monocyte gene expression signature in the early clinical course of Parkinson’s disease
(Submitter supplied) Recent studies suggest that the activation of the innate immune system is an integral part of Parkinson’s disease (PD) pathology. Monocytes have a critical role as effectors and regulators of the innate immune system, and a recent expression quantitative trait locus (eQTL) study links monocytes to PD. Patients diagnosed with PD according to the National Institute of Neurological Disorders and Stroke  diagnostic criteria for PD were included. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88888/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349023
Series		Accession: GSE88888	ID: 200088888

1564. Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL20301 84 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120887/
Series		Accession: GSE120887	ID: 200120887

1565. Inherent DNA binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin (RNA-seq)
(Submitter supplied) Hypoxia inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-a isoforms, HIF-1a and HIF-2a, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1b to activate a broad range of transcriptional responses. Here we report on the pan-genomic distribution of isoform-specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF-a isoform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494832
Series		Accession: GSE120886	ID: 200120886

1566. Transcriptomic Profile of OCI-AML-20 Cell Line
(Submitter supplied) Acute myeloid leukemia (AML) is a complex, heterogeneous disease with variable outcomes following curative intent chemotherapy. AML with inv(3) is a genetic subgroup characterized by low response rate to induction type chemotherapy and hence is among the worst long term survivorship of the AMLs. Here, we present RNA-Seq transcriptome data from OCI-AML-20, a new AML cell line with inv(3) and deletion of chromosome 7.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494672
Series		Accession: GSE120834	ID: 200120834

1567. Defining T cell states associated with response to checkpoint immunotherapy in melanoma
(Submitter supplied) we profiled 16,291 immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors, using single-cell transcriptomics.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120575/
Series		Accession: GSE120575	ID: 200120575

1568. Proteostasis by STUB1/HSP70 complex controls sensitivity to androgen receptor targeted therapy in advanced prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL570 9 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120006/
Series		Accession: GSE120006	ID: 200120006

1569. Proteostasis by STUB1/HSP70 complex controls sensitivity to androgen receptor targeted therapy in advanced prostate cancer (RNA-Seq)
(Submitter supplied) Constitutively active androgen receptor (AR) signaling confers resistance to AR-targeted therapies. Here we show that the ubiquitin-mediated proteolysis pathway plays a critical role in the degradation of AR and its variants, particularly variant 7 (AR-V7). AR/AR-V7 proteinhomeostasis (proteostasis) requires interaction of the E3 ubiquitin ligase STUB1 and HSP70complex. STUB1 disassociates AR/AR-V7 from HSP70, leading to AR/AR-V7 ubiquitination and degradation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120004/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491274
Series		Accession: GSE120004	ID: 200120004

1570. PARCB Project: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL21290 74 Samples
FTP download: GEO (BIGWIG, TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118207/
Series		Accession: GSE118207	ID: 200118207

1571. Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq)
(Submitter supplied) Small cell carcinomas from different tissues exhibit transcriptional and epigenetic convergence and suggest common vulnerabilities for therapies
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 36 Samples
FTP download: GEO (TAR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118206/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484869
Series		Accession: GSE118206	ID: 200118206

1572. Multi-Omic Molecular Profiling of Lung Cancer Risk in Chronic Obstructive Pulmonary Disease
(Submitter supplied) Chronic obstructive pulmonary disease (COPD) is a known risk factor for developing lung cancer suggesting that the COPD stroma contains factors supporting tumorigenesis. Since cancer initiation is complex we used a multi-omic approach to identify gene expression patterns that distinguish COPD stroma in patients with or without lung cancer. We obtained lung tissue from patients with COPD and lung cancer (tumor and adjacent non-malignant tissue) and those with COPD without lung cancer for proteomic and mRNA (cytoplasmic and polyribosomal) profiling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 66 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106899/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418402
Series		Accession: GSE106899	ID: 200106899

1573. Truncated O-glycan connection to Cancer: Depletion of O-glycosyltransferase C1GALT1 leads to early PDAC onset and metastasis
(Submitter supplied) Aberrant expression of truncated O-glycan structures, such as Tn and STn, is frequently observed in pancreatic ductal adenocarcinoma (PDAC). The focus of our study is to investigate the functional role of truncated O-glycans in PDAC progression and metastasis. Our study revealed that kmockout of C1GALT1 leads to increased expression of truncated glycans and accelerates PDAC progression and metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104607/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413293
Series		Accession: GSE104607	ID: 200104607

1574. Monitoring Nivolumab binding as a method to clarify the residual therapeutic effects and to characterize the immune profile in antibody bound T cells in previously treated non-small cell lung cancer patients
(Submitter supplied) The goal of this study is to evaluate immune profile in anti PD-1 antibody, Nivolumab, bound CD8 T cells vs Nivolumab unbound CD8 T cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393306
Series		Accession: GSE100860	ID: 200100860

1575. Development and Characterisation of Acquired Radioresistant Breast Cancer Cell Lines.
(Submitter supplied) Background: Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance.  Methods: Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494562
Series		Accession: GSE120798	ID: 200120798

1576. Atlas of RNA sequencing profiles of normal human tissues
(Submitter supplied) Comprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. There is a shortage now of the gene expression data for human healthy tissues. The available data can either lack biological replicates or represent tissues adjacent to tumors removed during surgery that have signs of pathology and inflammation. For the available limited collections of normal tissues from post mortal donors, there is a problem of data incompatibility, as different datasets were generated using different experimental platforms and cannot be merged in a single panel. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 165 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494560
Series		Accession: GSE120795	ID: 200120795

1577. TET2 coactivates gene expression through demethylation of enhancers
(Submitter supplied) The tet methylcytosine dioxygenase 2 (TET2) enzyme catalyzes the conversion of the modified DNA base 5-methylcytosine to 5-hydroxymethylcytosine. TET2 is frequently mutated or dysregulated in multiple human cancers, and loss of TET2 is associated with changes in DNA methylation patterns. Here, using newly developed TET2-specific antibodies and the estrogen response as a model system for studying the regulation of gene expression, we demonstrate that endogenous TET2 occupies active enhancers and facilitates the proper recruitment of ERalpha. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL18573 79 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120756/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494397
Series		Accession: GSE120756	ID: 200120756

1578. Migration through a small pore disrupts inactive chromatin organisation in neutrophil-like cells [RNA-seq]
(Submitter supplied) Background. Mammalian cells are flexible and can rapidly change shape when they contract, adhere, or migrate. Their nucleus must be stiff enough to withstand cytoskeletal forces, but flexible enough to remodel as the cell changes shape. This is particularly important for cells migrating through constricted space, where the nuclear shape must change in order to fit through. This happens many times in the life cycle of a neutrophil, which must protect its chromatin from damage and disruption associated with migration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475594
Series		Accession: GSE115632	ID: 200115632

1579. Optimal settings of mass spectrometry open search strategy for higher confidence
(Submitter supplied) More than half of the mass spectra could not be identified in most proteome mass spectrometry experiments. Various modifications have been considered as a major reason. Open search strategy was then introduced to solve this problem, however, lacking thorough quality assessment using independent information. Here, we used the “Suspicious Discovery Rate (SDR)” based on the translatome sequencing (RNC-seq) as an independent source to assess the proteome open search strategy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20795 GPL23227 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112623/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448556
Series		Accession: GSE112623	ID: 200112623

1580. Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by SNP array; Expression profiling by high throughput sequencing
Platforms: GPL23668 GPL11154 105 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101109/
Series		Accession: GSE101109	ID: 200101109

1581. Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [RNA-Seq]
(Submitter supplied) Ovarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (I, II) ovarian carcinomas (n=96) in relation to clinicopathological characteristics and clinical outcome, thereby identifying novel genetic features of ovarian carcinomas. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101108/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393722
Series		Accession: GSE101108	ID: 200101108

1582. Integrative epigenetic taxonomy of primary prostate cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 404 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120742/
Series		Accession: GSE120742	ID: 200120742

1583. Integrative epigenetic taxonomy of primary prostate cancer [RNA-Seq]
(Submitter supplied) The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. To comprehensively study the epigenetic landscape, we complemented RNA-seq with ChIP-seq for AR and histone modification marks (H3K27ac, H3K4me3, H3K27me3) in 100 primary prostate carcinomas. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 92 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494345
Series		Accession: GSE120741	ID: 200120741

1584. mRNA-seq for etoposide-treated TLP-knockdown cells
(Submitter supplied) We explored the mechanism by which TLP affects DNA damage response. We performed mRNA-seq analysis of non-treated and etoposide-treated samples in control and TLP-knockdown cells. We show that TLP is critical for global transcriptional repression after double-strand DNA breaks (DSBs).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120734/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494328
Series		Accession: GSE120734	ID: 200120734

1585. TRPS1 is a lineage-specific transcriptional dependency in breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms: GPL18573 GPL13534 193 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114600/
Series		Accession: GSE114600	ID: 200114600

1586. TRPS1 is a lineage-specific transcriptional dependency in breast cancer [Seq]
(Submitter supplied) We performed an unbiased cell viability-based pooled shRNA screen on 59 cell lines to identify novel epigenetic and transcriptional dependencies of multiple cancer types, including leukemia, neuroblastoma, breast, colorectal, prostate, and rhabdoid tumors. Here, we identified Tricho-Rhino-Phalangeal Syndrome Type I protein (TRPS1) as one of the most significant hits specific for breast cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 132 Samples
FTP download: GEO (CSV, GCT, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114597/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471883
Series		Accession: GSE114597	ID: 200114597

1587. KDM5B links cellular transcriptome heterogeneity to therapy resistance
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 333 Samples
FTP download: GEO (BED, BROADPEAK, BW, NARROWPEAK, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104988/
Series		Accession: GSE104988	ID: 200104988

1588. KDM5B links cellular transcriptome heterogeneity to therapy resistance (inDrop)
(Submitter supplied) The KDM5B histone H3 lysine 4 (H3K4) demethylase has been implicated in therapy resistance in multiple cancer types including breast cancer, but the underlying mechanism is poorly defined. Here we show that inhibition of KDM5B activity increases sensitivity to anti-estrogens by modulating estrogen-receptor (ER) signaling. Conversely, acquired resistance to KDM5 inhibitors leads to gain of ER chromatin binding and estrogen-independent growth. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104987/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414337
Series		Accession: GSE104987	ID: 200104987

1589. KDM5B links cellular transcriptome heterogeneity to therapy resistance (RNA-Seq)
(Submitter supplied) The KDM5B histone H3 lysine 4 (H3K4) demethylase has been implicated in therapy resistance in multiple cancer types including breast cancer, but the underlying mechanism is poorly defined. Here we show that inhibition of KDM5B activity increases sensitivity to anti-estrogens by modulating estrogen-receptor (ER) signaling. Conversely, acquired resistance to KDM5 inhibitors leads to gain of ER chromatin binding and estrogen-independent growth. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 118 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104985/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414329
Series		Accession: GSE104985	ID: 200104985

1590. Gene Expression Profiling of SPOP Knocked Down Cell
(Submitter supplied) SPOP is one of the most frequent mutated genes in prostate cancer. In the current study, we identified CCNE1 as its substrate. SPOP directly interacts with CCNE1, poly-ubiquitinates CCNE1 in vivo and in vitro, and represses cancer-related phenotypes induced by CCNE1 expression. Thus, we reveal a new mechanism for SPOP in repressing prostate cancer tumorigenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100743/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392902
Series		Accession: GSE100743	ID: 200100743

1591. Differential analysis of gene expression profiles in peripheral blood cells of patients with cervical lesions
(Submitter supplied) Using RNA-sequencing analysis of peripheral blood cells from 11 cervical cancer patients, 21 cervical intraepithelial neoplasia patients and 19 healthy controls, we identified a group of differentially expressed genes. A real time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was applied to the validation of candidate markers in the blood of 115 patients and 46 healthy controls. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 51 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120691/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA494155
Series		Accession: GSE120691	ID: 200120691

1592. Alternative splicing analysis of pediatric B-cell acute lymphoblastic leukemia compared to normal bone marrow derived pro-B cells
(Submitter supplied) Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 38 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115656/
Series		Accession: GSE115656	ID: 200115656

1593. Bone marrow derived human B cells [normal proB]
(Submitter supplied) Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115655/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475684
Series		Accession: GSE115655	ID: 200115655

1594. Aberrant splicing in B-cell acute lymphoblastic leukemia [cell line]
(Submitter supplied) Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115654/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475682
Series		Accession: GSE115654	ID: 200115654

1595. Aberrant splicing in B-cell acute lymphoblastic leukemia [B-ALL]
(Submitter supplied) Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing them to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ~100 SFs, e.g. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115653/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475683
Series		Accession: GSE115653	ID: 200115653

1596. Transcriptome analysis of the HepG2 cells expressing hepatic transcription factors
(Submitter supplied) In order to elucidate an anticancer function of some hepatic transcription factors (TFs), we induced the three hepatic TFs: HNF1A, HNF4A, and FOXA3, into a hepatocellular carcinoma cell line, HepG2, with some combination.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115423/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474931
Series		Accession: GSE115423	ID: 200115423

1597. RNA transcriptome sequencing analysis of SGC-7901 cells transfected with ENST00000431060 shRNA or control shRNA
(Submitter supplied) RNA transcriptome sequencing analysis was performed in SGC-7901 cells that were transfected with ENST00000431060 shRNA or control shRNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112586/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448373
Series		Accession: GSE112586	ID: 200112586

1598. Canonical and non-canonical regulatory roles of androgen receptor variant 7 in prostate cancer
(Submitter supplied) The androgen receptor splice variant 7 (AR-V7) lacks the ligand-binding domain; is detected with increased frequency in advanced prostate cancer and is postulated to be one crucial mechanism for disease progression and therapeutic resistance to androgen deprivation in castration–resistant prostate cancer (CRPC). Targeting AR-V7 or unique downstream targets could provide novel therapeutic approaches for CRPC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 36 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363052
Series		Accession: GSE94013	ID: 200094013

1599. ATO treatment on mesenchymal stem cells (MSCs) interacting breast cancer cells
(Submitter supplied) Based on next generation RNA-seq, we examed Arsenic trioxide treatment (ATO) effect on MSCs-interacting MCF7 cells in 3D cultures. We found gap junction protein Cx43 is dramatically downregulated after ATO treatment..
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platform: GPL19415 6 Samples
FTP download: GEO (CSV, RDATA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118923/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487341
Series		Accession: GSE118923	ID: 200118923

1600. Transcriptome of human non-functional pancreatic neuroendocrine tumors (PanNETs)
(Submitter supplied) The most commonly mutated genes in pancreatic neuroendocrine tumors (PanNETs) are ATRX, DAXX, and MEN1. Little is known about the cells-of-origin for non-functional neuroendocrine tumors. Here, we genotyped 64 PanNETs for mutations in ATRX, DAXX, and MEN1 and found 37 tumors (58%) carry mutations in these three genes (A-D-M mutant PanNETs) and this correlates with a worse clinical outcome than tumors carrying the wild-type alleles of all three genes (A-D-M WT PanNETs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118014/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484008
Series		Accession: GSE118014	ID: 200118014

1601. Gene expression and methylation profile of Human non-functional Pancreatic neuroendocrine tumors (PanNETs)
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Methylation profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL571 GPL11154 GPL13534 112 Samples
FTP download: GEO (CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117853/
Series		Accession: GSE117853	ID: 200117853

1602. An assessment of prognostic immunity markers in breast cancer
(Submitter supplied) We used Targeted RNA-seq to generate a gene expression data set of the 72-gene panel (TARGETSEQ) including 483 targeted RNA-seq data of 225 breast cancer FFPE samples from Shanghai and 258 breast cancer FFPE samples from UNC at Chapel Hill. The identified gene panel and risk evaluation model iRDM were developed in training data set AFFY1951 (p<0.0001, n=1951) and further  validated in two other published gene expression datasets including Illumina beads array data METABRIC (p<0.0001, n=1997) and whole transcriptomic mRNA-seq data TCGA (p=0.00019, n=996) and in our own targeted RNA-seq data TARGETSEQ (p<0.0001, n=303) (of 483 RNA-seq samples, 303 with survival data). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL15520 GPL18573 483 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454288
Series		Accession: GSE113863	ID: 200113863

1603. Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome
(Submitter supplied) Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9442 GPL18573 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108773/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428518
Series		Accession: GSE108773	ID: 200108773

1604. Discovery of inhibitors of the HSP90-Calcineurin-NFAT pathway against glioblastoma
(Submitter supplied) We report the application of mRNA sequencing technology for high-throughput profiling of genes expression changes in U87 glioblastoma cells after treatment with compound YZ129 that we identified in our screen. By analyzing the total mRNA sequencing between YZ129 treatment group and the DMSO control group, we identified that 181 genes were significantly downregulated (changed >2 folds), while 226 genes were significantly upregulated (changed >2 folds). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108749/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428485
Series		Accession: GSE108749	ID: 200108749

1605. 4 NSCLC cell lines treated with GDC-0973, AZ-628 or a combination of both
(Submitter supplied) RNA was purified cancer cell lines. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013114
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427330
Series		Accession: GSE108464	ID: 200108464

1606. RNA-seq analysis of uveal melanoma cells treated with FR900359
(Submitter supplied) FR900359 is an allosteric inhibitor of Gq. 92.1 uveal melanoma cells, which are driven by constitutively active Gq, were treated with 100 nM FR900359 or vehicle for 1 day and 3days. RNA-seq was performed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103761/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA406947
Series		Accession: GSE103761	ID: 200103761

1607. Expression profiling by high throughput sequencing and transcriptome-wide association study study the metabolic mechanism of the formation of atorvastatin lactone and the risk to statin-induced myotoxicity
(Submitter supplied) Statin-induced myotoxicity (SIM) is one of the principal reasons for atorvastatin (AT) non-adherence and/or discontinuation, contributing to adverse cardiovascular outcomes. To date, the genetic mechanism of SIM is far from well-illustrated. Published data in vitro and in vivo indicated that atorvastatin lactone (ATL) is the key metabolite to induce myotoxicity. We therefore hypothesis that genetic variants increasing the formation of ATL can increase the risk to statin-induced myotoxicity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 53 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87592/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345313
Series		Accession: GSE87592	ID: 200087592

1608. Genomic Analysis of DNA Repair Genes and Androgen Signaling in Prostate Cancer
(Submitter supplied) Abstract    Background. The cellular effects of androgen are transduced through the androgen receptor, which controls the expression of genes that regulate biosynthetic processes, cell growth, and metabolism. Androgen signaling also impacts DNA damage signaling through mechanisms involving gene expression and transcription-associated DNA damaging events. Defining the contributions of androgen signaling to DNA repair is important for understanding androgen receptor function, and it also has important translational implications. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493954
Series		Accession: GSE120660	ID: 200120660

1609. RNA-seq analysis of control and NRDE2-depleted breast cancer cells
(Submitter supplied) Purpose: investigate transcriptomic changes following depletion of the NRDE2 gene Methods: MDA-MB-231 breast cancer cells were transfected with 20nM control or NRDE2-targeting siRNAs, and RNA was collected after 48h for RNA-seq analysis Results: We analyzed si-Control and si-NRDE2-treated samples in triplicate (~46-64 million reads per sample) and find that the near-complete loss of NRDE2 results in generally modest changes in gene expression, with only 84 genes deregulated >2-fold. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119827/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490376
Series		Accession: GSE119827	ID: 200119827

1610. Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny
(Submitter supplied) We report here the multi-omics analysis of esthesioneuroblastomas, which is a rare cancer arising from the olfactory bulb. We discovered ENB can be grouped in two subtypes, namely basal and neural ENBs. We also uncovered high rates of mutations (~35%) in basal ENB subgroup.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118995/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487796
Series		Accession: GSE118995	ID: 200118995

1611. DNA and Histone Methyltransferase Inhibitors Cooperate to Increase Viral Mimicry in Ovarian Cancer Cells
(Submitter supplied) Total RNA sequenceing method was used to compare the differential expression of genes in A2780, CAOV3, PEO14, and OAW42 cells with G9Ai, 5-aza-CdR and combination treatment compared to untreated cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 32 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422873
Series		Accession: GSE108223	ID: 200108223

1612. Transcriptomic response to etoposide treatment in immune cell lines
(Submitter supplied) RNA-seq analysis of the effects of etoposide treatment on transcriptomes of human pre-B, mature B, T and myeloid cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 34 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120612/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493754
Series		Accession: GSE120612	ID: 200120612

1613. RNA-Seq data of NCI-H82 cells expressing a Dox-On pRB (pTripZ RB1) grown in the presence or absence of DOX and then treated with vehicle or AZD2811.
(Submitter supplied) We report changes in gene expression in response to reexpression of pRB in NCI-H82 cells and how AZD2811 differentially affects the transcriptome of these cells depending on whether or not pRB is expressed.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120562/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493571
Series		Accession: GSE120562	ID: 200120562

1614. TERT Promoter DNA methylation landscape in human cancer cell lines and tumors
(Submitter supplied) We assessed methylation landscape near the human TERT promoter in various normal samples and tumor samples, to assess the unique hypermethylation phenotype that exist in human cancers
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL15520 129 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493239
Series		Accession: GSE120511	ID: 200120511

1615. Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18460 59 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107612/
Series		Accession: GSE107612	ID: 200107612

1616. Transcriptome analysis of PRMT6 knock-out in NT2/D1 cells
(Submitter supplied) Whole transcriptome for PRMT6 knock-out and control NT2/D1 cells with and without ATRA (all-trans retinoic acid) was sequenced. These samples were compared to each other to find differentially regulated genes and PRMT6-dependent transcriptome in pluripotency and differentiating cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107611/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420764
Series		Accession: GSE107611	ID: 200107611

1617. RNA-seq of exosomes identifies lncRNA profiles that distinguish early-stage esophageal squamous cell carcinoma (ESCC) from non-malignant esophagitis
(Submitter supplied) We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and  esophagitis.  By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL21290 18 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414172
Series		Accession: GSE104926	ID: 200104926

1618. Next Generation Sequencing Analyzes Transcriptome after  TMEM126A overexpression and knockdown
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify the differential expression genes after TMEM126A overexpression or knockdown. Methods:Total cell mRNA profiles of TMEM126A-knockdown MDA-MB-231 cells (sh-NC vs shT126A) and TMEM126A-overexpression MCF10-Ca1a cells(pCDH vs T126A) were generated by deep sequencing, using Illumina HiSeq 2500. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120468/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA493103
Series		Accession: GSE120468	ID: 200120468

1619. Transcriptomes change differerntly in differernt cancer cells upon EPZ-6438 treatment
(Submitter supplied) Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to find out the difference between EZH2 inhibitor treatment and DMSO group in each cancer cell line, and find the relationship between transcriptomes change and drug sensivitity. Methods: mRNA profiles of cell lines were generated using  Illumina PE150, then GSEA was used for cellular pathways analysis Results:  The result showed 53 common oncogenic signatures were enriched in RNA-seq data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119088/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488071
Series		Accession: GSE119088	ID: 200119088

1620. Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation [iCLIP-seq]
(Submitter supplied) We show here that SDOS interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS binds directly RNA in living cells. Combining individual gene expression profiling, nucleotide cross-linking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118049/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484188
Series		Accession: GSE118049	ID: 200118049

1621. Protein Syndesmos is a novel RNA binding protein that regulates primary cilia formation [Ribo-seq]
(Submitter supplied) We show here that NUDT16L1/TIRR/Syndesmos (SDOS) interacts with another important cancer-linked protein, the chaperone TRAP1, associates with actively translating polyribosomes and represses translation. Moreover, we demonstrate that SDOS binds directly RNA in living cells. Combining individual gene expression profiling, nucleotide cross-linking and immunoprecipitation (iCLIP), and ribosome profiling, we discover several crucial pathways regulated post-transcriptionally by SDOS.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117998/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484185
Series		Accession: GSE117998	ID: 200117998

1622. The NFkB subunit RELA is a master transcriptional regulator of the committed epithelial-mesenchymal transition in airway epithelial cells
(Submitter supplied) The epithelial-mesenchymal transition (EMT) is a multistep dedifferentiation program important in tissue repair. Here, we examined the role of the transcriptional regulator NFkB in EMT of human primary small airway epithelial cells (hSAECs). Surprisingly, transforming growth factor β (TGFβ) activated NFkB/RELA proto-oncogene, NFkB subunit (RELA) translocation within 1 day of stimulation, yet induction of its downstream gene regulatory network occurred only after 3 days. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 18 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84135/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328132
Series		Accession: GSE84135	ID: 200084135

1623. Intrinsic immunity employs 2’,5’-oligoadenylate signaling to establish privileged translation of interferons β and l
(Submitter supplied) RNAseq of control vs poly-IC treated A549 cells shows IFN induction.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120355/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492872
Series		Accession: GSE120355	ID: 200120355

1624. Systematic analysis of gene expression profiles controlled by hnRNP Q and hnRNP R, two closely related human heterogeneous nuclear ribonucleoproteins.
(Submitter supplied) hnRNPQ and the highly related hnRNPR regulate expression of genes related with neuronal and immune functions
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TSV, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114165/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA465747
Series		Accession: GSE114165	ID: 200114165

1625. Differences in RNA expression between primary and metastatic colon tumor
(Submitter supplied) Here, we report the genomic-scale characterization of metastatic colon cancer transcriptome. Fresh-frozen samples was used to asses differences between normal colon, primary colon tumor an liver metastasis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89393/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352049
Series		Accession: GSE89393	ID: 200089393

1626. MYC Targeted Long Noncoding RNA DANCR Promotes Cancer in Part by Reducing p21 Levels.
(Submitter supplied) p493 RNA-seq in the MYC on and MYC off conditions
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120246/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492293
Series		Accession: GSE120246	ID: 200120246

1627. Human Bone Marrow Assessment by Single Cell RNA Sequencing, Mass Cytometry and Flow Cytometry [scRNA]
(Submitter supplied) New techniques for single-cell analysis have led to insights into hematopoiesis and the immune system, but the ability of these techniques to cross-validate and reproducibly identify the biological variation in diverse human samples is currently unproven. We therefore performed a comprehensive assessment of human bone marrow cells using both single-cell RNA sequencing and multiparameter flow cytometry from twenty healthy adult human donors across a broad age range. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 25 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492227
Series		Accession: GSE120221	ID: 200120221

1628. mRNA circularization by METTL3-eIF3h enhances translation
(Submitter supplied) N6-methyladenosine (m6A) modification of mRNA catalyzed by METTL3 is enriched at a subset of stop codons. METTL3 can promote translation but the mechanism and widespread relevance remain unknown. Here we show that METTL3 enhances translation only when tethered to reporter mRNA at sites close to the stop codon supporting a mRNA looping mechanism for ribosome recycling and translational control. Electron microscopy revealed the topology of individual polyribosomes with single METTL3 foci found in close proximity to 5’ cap-binding proteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 56 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481680
Series		Accession: GSE117299	ID: 200117299

1629. UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking
(Submitter supplied) Assuming that functional lncRNAs form larger ribonucleoprotein complex and thus are easily crosslinked to proteins upon UV-irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after the UV-irradiation and phenol chloroform extraction (UPA-Seq)
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 GPL17021 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114789/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472627
Series		Accession: GSE114789	ID: 200114789

1630. GATA2 monoallelic expression underlies reduced penetrance in inherited GATA2-  mutated MDS/AML
(Submitter supplied) Although familial myelodysplasia and acute myeloid leukemia (MDS/AML) is rare, its true prevalence is likely underestimated due to wide variations in the age of onset, disease latency and outcome between and within families, with some mutation carriers remaining asymptomatic into late adulthood. Reduced penetrance is a notable feature of germline GATA2 p.Thr354Met pedigrees. In this study, we demonstrate that silencing of the wildtype (WT) GATA2 allele discriminates between symptomatic and asymptomatic carriers and is linked with allele-specific differences in DNA methylation and H3K4me3 promotor deposition, providing a molecular explanation for the clinical heterogeneity observed within a GATA2-mutated AML family.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413065
Series		Accession: GSE104570	ID: 200104570

1631. Bulk RNA-seq U2OS cells treated with small molecules
(Submitter supplied) We report the transcriptional changes associated with treatment of U2OS osteosarcoma cell line with DMSO, AML108, AMN107, BGW675, JAA804, LEE837 and LHD510.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 72 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120222/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA492171
Series		Accession: GSE120222	ID: 200120222

1632. CDK4 inhibition diminishes p53 activation by Mdm2-antagonists
(Submitter supplied) CDK4 inhibitors have reached clinical approval for cancer therapy. In parallel, the p53 antagonist Mdm2 remains an attractive target for anti-cancer therapy, including numerous clinical studies. The genes encoding Mdm2 and CDK4 are frequently co-amplified in human malignancies, most notably in liposarcomas, suggesting their combined targeting for therapy. Here we show, however, that small compounds that inhibit Mdm2 and CDK4 antagonize each other rather than synergize in their cytotoxicity towards sarcoma cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (CSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450932
Series		Accession: GSE113369	ID: 200113369

1633. Subtype-specific regulatory network rewiring in acute myeloid leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL16791 75 Samples
FTP download: GEO (BEDGRAPH, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108316/
Series		Accession: GSE108316	ID: 200108316

1634. Subtype-specific regulatory network rewiring in acute myeloid leukemia [RNA-seq]
(Submitter supplied) Acute myeloid leukemia is a heterogeneous disease which is subdivided into different categories defined by disease-causing mutations in transcription factors, epigenetic regulators and signalling molecules. How different mutant regulators establish AML-specific transcriptional networks is unclear. Here we performed a comprehensive analysis of mutation-specific sets of cis-regulatory elements driving gene expression in AML blast cells from a carefully selected group of patients with alterations in genes encoding transcription factors (RUNX1, CEBPA) and signalling molecules (FTL3-ITD, RAS, NPM1). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 40 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108266/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423049
Series		Accession: GSE108266	ID: 200108266

1635. CD95/Fas ligand mRNA is toxic to cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20301 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103631/
Series		Accession: GSE103631	ID: 200103631

1636. CD95L mRNA is toxic to cells [SmallRNA.CD95L.50hrs.HeyA8]
(Submitter supplied) >80% of a large number of tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death that is characterized by the simultaneous activation of multiple death pathways and preferentially affects transformed and cancer stem cells. We now show that these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102780/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398657
Series		Accession: GSE102780	ID: 200102780

1637. CD95L mRNA is toxic to cells [SmallRNA_CD95L.50hrs.Drosha_ko]
(Submitter supplied) >80% of a large number of tested siRNAs and shRNAs targeting CD95 or CD95 ligand (CD95L) induce a form of cell death that is characterized by the simultaneous activation of multiple death pathways and preferentially affects transformed and cancer stem cells. We now show that these si/shRNAs kill cancer cells through canonical RNAi by targeting the 3’UTR of critical survival genes in a unique form of off-target effect. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102779/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398656
Series		Accession: GSE102779	ID: 200102779

1638. Expression analysis of genes modulated after knock-down of lncRNA CHROME.
(Submitter supplied) Thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome, many of which are not conserved in lower mammals. The majority of these lncRNAs remain functionally uncharacterized and may have important implications in human physiology and disease. Here, we identify a primate-specific lncRNA, CHROME, which is increased in the plasma and atherosclerotic plaques of individuals with coronary artery disease compared to healthy controls. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97469/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382139
Series		Accession: GSE97469	ID: 200097469

1639. Gene expression profiling of xenografts generated by lung metastasis screening models and HCCLM3 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120096/
Series		Accession: GSE120096	ID: 200120096

1640. Gene expression profiling of HCCLM3 cells: Control ASO vs SCARNA13 ASO
(Submitter supplied) Understanding the roles of ncRNAs in tumorigenesis and metastasis would establish avenues for the identification of diagnostic and therapeutic targets. We observed that lncRNA SNHG10 and its derived SCARNA13 were concomitantly upregulated in hepatocellular carcinoma (HCC) pulmonary metastases and associated with poor prognosis. Mechanistically, SCARNA13, modulated by SNHG10, facilitated the cell cycle and epithelial-mesenchymal transition (EMT) of HCC cells by promoting SOX9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120095/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491641
Series		Accession: GSE120095	ID: 200120095

1641. Gene expression profiling of xenografts generated by lung metastasis screening models
(Submitter supplied) Understanding the roles of ncRNAs in tumorigenesis and metastasis would establish avenues for the identification of diagnostic and therapeutic targets. We observed that lncRNA SNHG10 and its derived SCARNA13 were concomitantly upregulated in hepatocellular carcinoma (HCC) pulmonary metastases and associated with poor prognosis. Mechanistically, SCARNA13, modulated by SNHG10, facilitated the cell cycle and epithelial-mesenchymal transition (EMT) of HCC cells by promoting SOX9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 8 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120021/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA491643
Series		Accession: GSE120021	ID: 200120021

1642. Global gene expression profile of dasatinib-resistant RCH-ACV cells
(Submitter supplied) Purpose: Several ALL subtypes have been described depending on their karyotype, cell type, immunophenotype and gene-expression profile. Recently, a novel ALL subtype has been described and is characterized by expression of the pre-B cell receptor (pre-BCR). Interestingly, half of the cases is associated with the chromosomal translocation t(1:19), coding for the chimeric fusion protein E2A-PBX1, which is present in about 5% of pediatric and adult ALL. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97352/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381484
Series		Accession: GSE97352	ID: 200097352

1643. Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9115 GPL18573 46 Samples
FTP download: GEO (BEDGRAPH, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117259/
Series		Accession: GSE117259	ID: 200117259

1644. Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation [RNA-seq]
(Submitter supplied) Transcription factor NF-κB regulates cellular responses to environmental cues.  For many stimuli NF-κB resides only transiently in the nucleus.  Consequently, time-dependent transcriptional outputs are a fundamental feature of NF-κB activation.  Here we identify mechanisms that direct kinetic patterns of NF-κB-dependent gene expression and transcriptional outcomes in response to a transient NF-κB-inducing stimulus in B cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117254/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481546
Series		Accession: GSE117254	ID: 200117254

1645. Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 17 Samples
FTP download: GEO (BW, NARROWPEAK, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106565/
Series		Accession: GSE106565	ID: 200106565

1646. Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [RNA-seq]
(Submitter supplied) Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that the transcription factors TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. Our recent study have identified TP63 and SOX2 as super-enhancer-associated genes. However, functional consequences of their frequent co-localization at super-enhancers region remains unexplored. Here, ChIP-seq result indicated TP63 and SOX2 co-occupied peaks are significantly located the super enhancer region compare with unique of TP63 and SOX2 signaling, and combined RNA-seq analyses of different types of SCCs reveal that TP63 and SOX2 cooperatively regulate expression of the super-enhancer-associated the long non-coding RNA (lncRNA) gene, CCAT1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417255
Series		Accession: GSE106564	ID: 200106564

1647. High-throughput RNAi cell viability screen to identify selective targets for EWS-FLI1 positive Ewing sarcoma
(Submitter supplied) We have performed a high-throughput RNA interference screen to identify targets inhibiting EWS-FLI1 driven cell proliferation in Ewing sarcoma cells. EWS-FLI1 expressing A673 Ewing sarcoma cells were screened both in presence and absence of EWS-FLI1 shRNA induction with druggable siRNA library. Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest anti-proliferative hit identified only in presence of EWS-FLI1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE73nnn/GSE73092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA296043
Series		Accession: GSE73092	ID: 200073092

1648. Role of BET proteins in YAP/TAZ-dependent transcription
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 57 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102409/
Series		Accession: GSE102409	ID: 200102409

1649. Role of BET proteins in YAP/TAZ-dependent transcription [RNA-seq 2]
(Submitter supplied) We compared the impact of small molecules on the transcriptional profile of triple negative breast cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102408/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397710
Series		Accession: GSE102408	ID: 200102408

1650. Role of BET proteins in YAP/TAZ-dependent transcription [RNA-seq 1]
(Submitter supplied) We performed RNA-seq experiments to identify YAP/TAZ target genes in triple negative breast cancer cells, and evaluate the relevance of BET proteins for their expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102407/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397707
Series		Accession: GSE102407	ID: 200102407

1651. Molecular Determinants of Post-Mastectomy Breast Cancer Recurrence
(Submitter supplied) Breast cancer (BC) adjuvant therapy after mastectomy in the setting of 1-3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated molecular aberrations in primary cancers associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to non-recurrent controls.  We identified 115 HER2 negative, therapy naïve, T 1-3 and N 0-1 BC patients treated with mastectomy but no post-mastectomy radiotherapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 131 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119937/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490741
Series		Accession: GSE119937	ID: 200119937

1652. Identification of human gene expression induced by 4MU-xyloside treatment
(Submitter supplied) The Golgi stress response is a homeostatic mechanism that augments the functional capacity of the Golgi apparatus when Golgi function becomes insufficient (Golgi stress). Three response pathways of the Golgi stress response have been identified in mammalian cells, the TFE3, HSP47 and CREB3 pathways, which augment the capacity of specific Golgi functions such as N-glycosylation, anti-apoptotic activity and pro-apoptotic activity, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119909/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490660
Series		Accession: GSE119909	ID: 200119909

1653. mRNA expression analysis of human lung cancer cell line CUTO-3 and colorectal cancer cell line KM12-luc treated with TRK inhibitor CH7057288
(Submitter supplied) CUTO-3 and KM12-luc cell lines were treated with DMSO or 1 uM CH7057288 for 4 and 24 hours. Cellular RNA was extracted, processed to generate an mRNA library, and sequenced from both ends of the library using HiSeq 2500 Sequencing System. RSEM software was used to align reads against RefSeq transcripts and calculate expression values (FPKM) for each gene.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119900/
Series		Accession: GSE119900	ID: 200119900

1654. Epigenomic analysis of micro-dissected human liver reveals principles of zonated morphogenic and metabolic control
(Submitter supplied) To investigate the underlying molecular principles of metabolic and morphogenic zonation of the human liver lobule, we generated an integrated epigenetic map across three zones (pericentral, intermediate and periportal) by methylation and transcriptomic analysis of hepatocytes captured by laser micro-dissection. We observe a deep link between epigenetic zonation of human liver and a zonated expression of metabolic and morphogenic pathways: Key transcriptionally zonated enzymes in xenobiotic and glutamine metabolism show a strong anticorrelated methylation gradient indicating that zonal expression of these genes is partly controlled by epigenetic programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL16791 114 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414905
Series		Accession: GSE105127	ID: 200105127

1655. SWI/SNF component ARID1A restrains pancreatic neoplasia formation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119859/
Series		Accession: GSE119859	ID: 200119859

1656. Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer
(Submitter supplied) In this study, we used RNA-seq to investigate the transcriptomic (mRNA and miRNA) profiles of pancreatic cancer in 10 paired tumor and normal pancreatic samples from patients
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 40 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119794/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA490335
Series		Accession: GSE119794	ID: 200119794

1657. Transcriptomic profile of Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)
(Submitter supplied) Squamous cell carcinoma (SCC) is a common cancer with global public health burden that arises from ESPCs in the skin or mucosa. To understand how genetic risk factors lay the foundation for SCC and develop effective prevention strategies, it is critical to understand the biology of ESPCs. Extreme predisposition to SCC is a hallmark of FA, an inherited disorder caused by germline loss-of-function mutations in any of 22 genes associated with the FA DNA repair pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117362/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481882
Series		Accession: GSE117362	ID: 200117362

1658. The IMiDs, through loss of Ikaros and Aiolos, primes myeloma cells for daratumumab mediated killing by upregulation of CD38
(Submitter supplied) Recent studies have demonstrated that the immunomodulatory drugs (IMiDs) lead to the degradation of the transcription factors Ikaros and Aiolos. However, why their loss subsequently leads to multiple myeloma (MM) cell death remains unclear. Using CRISPR-Cas9 genome editing, we have deleted IKZF1 and IKZF3 in human MM cell lines to gain further insight into their downstream gene regulatory networks. Our findings strongly support the central role of Ikaros and Aiolos in the action of the IMiDs. Inactivation of either factor alone recapitulates the cell intrinsic action of the IMiDs, resulting in cell cycle arrest and induction of apoptosis. Furthermore, evaluation of the transcriptional changes resulting from their loss demonstrates striking overlap with lenalidomide treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113031/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449831
Series		Accession: GSE113031	ID: 200113031

1659. High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103730/
Series		Accession: GSE103730	ID: 200103730

1660. High-resolution liver cancer genomic profiling links etiology, epigenetic and mutation signatures [RNA-Seq]
(Submitter supplied) Purpose: This study unravel the mechanisms that link viral infection and cancer Methods:Human HCC cell line and HCC liver FFPE samples from HCC patients from three etiology groups- HBV, HCV infection, or neither were taken to explore their genomic DNA in two aspects: The HCC genomic mutations within the exons of 224 candidate genes, frequently mutated in HCC, using SureSelect™ Target Enrichment System kit and the transient response of liver cells to HCV infection, in genome wide histone modifications and gene expression, as demonstrated by ChIP-Seq and RNA-Seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA406886
Series		Accession: GSE103729	ID: 200103729

1661. Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk [RNA-seq]
(Submitter supplied) Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies (GWAS), efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Toward that end, experiments reported here extend our investigation of the disease mechanism of CAD associated gene SMAD3, a central transcriptional intermediate in the TGFb pathway, investigating its role in smooth muscle biology. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115318/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474526
Series		Accession: GSE115318	ID: 200115318

1662. 6mer seed toxicity in tumour suppressive microRNAs
(Submitter supplied) 6mer seed toxicity in tumour suppressive microRNAs
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 18 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111379/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436742
Series		Accession: GSE111379	ID: 200111379

1663. Total RNA-seq in a primary T-ALL patient cohort
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 25 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110636/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434176
Series		Accession: GSE110636	ID: 200110636

1664. Total RNA-seq in ALL-SIL upon TLX1 knockdown
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110635/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434175
Series		Accession: GSE110635	ID: 200110635

1665. Total RNA-seq in ALL-SIL upon JQ1 inhibition
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110634/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434173
Series		Accession: GSE110634	ID: 200110634

1666. PolyA+ RNA-seq in a primary T-ALL patient cohort
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 60 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110633/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434174
Series		Accession: GSE110633	ID: 200110633

1667. PolyA+ RNA-seq in ALL-SIL upon TLX1 knockdown
(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434171
Series		Accession: GSE110632	ID: 200110632

1668. Activating PAX Gene Family Paralogs to Complement PAX5 Leukemia Driver Mutations
(Submitter supplied) PAX5, one of nine members of the mammalian paired box (PAX) family of transcription factors, plays an important role in B cell development. Approximately one-third of individuals with pre-B acute lymphoblastic leukemia (ALL) acquire heterozygous inactivating mutations of PAX5 in malignant cells, and heterozygous germline loss-offunction PAX5 mutations cause autosomal dominant predisposition to ALL. At least in mice, Pax5 is required for pre-B cell maturation, and leukemic remission occurs when Pax5 expression is restored in a Pax5-deficient mouse model of ALL. Together, these observations indicate that PAX5 deficiency reversibly drives leukemogenesis. PAX5 and its two most closely related paralogs, PAX2 and PAX8, which are not mutated in ALL, exhibit overlapping expression and function redundantly during embryonic development. However, PAX5 alone is expressed in lymphocytes, while PAX2 and PAX8 are predominantly specific to kidney and thyroid, respectively. We show that forced expression of PAX2 or PAX8 complements PAX5 loss-of-function mutation in ALL cells as determined by modulation of PAX5 target genes, restoration of immunophenotypic and morphological differentiation, and, ultimately, reduction of replicative potential. Activation of PAX5 paralogs, PAX2 or PAX8, ordinarily silenced in lymphocytes, may therefore represent a novel approach for treating PAX5-deficient ALL. In pursuit of this strategy, we took advantage of the fact that, in kidney, PAX2 is upregulated by extracellular hyperosmolarity. We found that hyperosmolarity, at potentially clinically achievable levels, transcriptionally activates endogenous PAX2 in ALL cells via a mechanism dependent on NFAT5, a transcription factor coordinating response to hyperosmolarity. We also found that hyperosmolarity upregulates residual wild type PAX5 expression in ALL cells and modulates gene expression, including in PAX5-mutant primary ALL cells. These findings specifically demonstrate that osmosensing pathways may represent a new therapeutic target for ALL and more broadly point toward the possibility of using gene paralogs to rescue mutations driving cancer and other diseases.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432203
Series		Accession: GSE109860	ID: 200109860

1669. Amiloride, an old diuretic drug, is a potential therapeutic agent for multiple myeloma
(Submitter supplied) The introduction of novel therapeutic agents has considerably improved the median survival of patients with multiple myeloma (MM). However, the natural history of the disease is characterized by continuous relapses over time. As a consequence, the development of new drugs is still required to treat MM recurrence. Here, we report for the first time the potent anti-myeloma activity of amiloride, an old potassium-sparing diuretic approved for the treatment of hypertension and edema due to heart failure. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95077/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375938
Series		Accession: GSE95077	ID: 200095077

1670. Integrating the Epigenome to Identify Novel Drivers of Hepatocellular Carcinoma
(Submitter supplied) Gene expression, histone modification, DNA methylation, and DNA hydroxymethylation from normal, cirrhotic, and HCC livers
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL16791 55 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445291
Series		Accession: GSE112221	ID: 200112221

1671. Defective transcription elongation in a subset of cancers confers immunotherapy resistance
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
5 related Platforms 32 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119679/
Series		Accession: GSE119679	ID: 200119679

1672. Defective transcription elongation in a subset of cancers confers immunotherapy resistance (human cell lines RNA-Seq)
(Submitter supplied) The nature and the role of global transcriptional deregulations in cancers are not fully understood. We report a phenotype in a significant portion of cancers characterized by widespread defects in mRNA transcription elongation (TE). Cancers with TE defects (TEdeff) were characterized by spurious transcription and defective mRNA processing, specifically in a large set of genes characterized by long genomic length, poised promoters and inducible expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119678/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489892
Series		Accession: GSE119678	ID: 200119678

1673. Defective transcription elongation in a subset of cancers confers immunotherapy resistance (BGI12 RNA-Seq)
(Submitter supplied) The nature and the role of global transcriptional deregulations in cancers are not fully understood. We report a phenotype in a significant portion of cancers characterized by widespread defects in mRNA transcription elongation (TE). Cancers with TE defects (TEdeff) were characterized by spurious transcription and defective mRNA processing, specifically in a large set of genes characterized by long genomic length, poised promoters and inducible expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119674/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489891
Series		Accession: GSE119674	ID: 200119674

1674. Extraction-Free Whole Transcriptome Profiling from Specific Subareas of Unstained or H&E Stained FFPE Tissues
(Submitter supplied) We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq™, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. more...
Organism:	Rattus norvegicus; Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL20084 GPL19057 155 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489794
Series		Accession: GSE119630	ID: 200119630

1675. Translation of upstream open reading frames in a model of neuronal differentiation
(Submitter supplied) Upstream open reading frames (uORFs) initiate translation within mRNA 5’ leaders,and have the potential to altermain coding sequence(CDS) translationontranscripts in which they reside. Ribosome profiling(RP)studies suggest that translating ribosomes are pervasive within 5’ leadersacross model systems. However, the significance of this observationremains unclear. To explore a role for uORF usage in neuronal differentiation, we performed RP on undifferentiated and differentiated human neuroblastoma cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119615/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489713
Series		Accession: GSE119615	ID: 200119615

1676. Comparison of Transcriptomes between A549 and H23 Cells
(Submitter supplied) We profiled transcriptomes in human lung cancer cell lines H23 and A549 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489445
Series		Accession: GSE119513	ID: 200119513

1677. Effects of Bloom RNAi on Transcriptomes in A549 Cells
(Submitter supplied) We profiled transcriptomes in human lung cancer cell line A549 when the expression of Bloom was knockdown by the siRNA specific to Bloom.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489443
Series		Accession: GSE119512	ID: 200119512

1678. Effects of HOTAIR RNAi on Transcriptomes in T47D Cells
(Submitter supplied) We profiled transcriptomes in human breast cancer cell line T47D when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489444
Series		Accession: GSE119511	ID: 200119511

1679. Effects of HOTAIR RNAi on Transcriptomes in H23 Cells
(Submitter supplied) We profiled transcriptomes in human lung cancer cell line H23 when the expression of HOTAIR was knockdown by the siRNA specific to an HOTAIR isoform HOTAIR-N (NR_047517).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489442
Series		Accession: GSE119510	ID: 200119510

1680. Expression analysis of PC3 cells treated with scramble AON or AON directed against MBNL1
(Submitter supplied) We transfected PC3 cells with 100nM of a scrambled antisense oligonucleotide (AON) and an AON directed against MBNL1 exon 7 (36 basepairs) in order to skip the latter. Cells were harvested at 72h post-transfection and RNAseq was performed with ribozero depletion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471253
Series		Accession: GSE114383	ID: 200114383

1681. The expression profile of CD4lowHLA-G+ T cells
(Submitter supplied) The aim of the dataset was to demonstrate that CD4lowHLA-G+ T cells were not TH2 cells by comparing the expression profiles of CD4lowHLA-G+ T cells to those of TH2 cells induced from CD4+ T cells under TH2-polarzing conditions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL20795 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401810
Series		Accession: GSE103537	ID: 200103537

1682. Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm 
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL24082 GPL11154 60 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104974/
Series		Accession: GSE104974	ID: 200104974

1683. Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm [RNA-Seq]
(Submitter supplied) In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104973/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414291
Series		Accession: GSE104973	ID: 200104973

1684. Genome-wide profiling of siRNA targeting EWS-FLI1 in TC32 Ewing sarcoma cell line
(Submitter supplied) Identification of genes and pathways that were influenced by knock-down EWS-FLI1 in TC32 Ewing sarcoma cell line.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103843/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407227
Series		Accession: GSE103843	ID: 200103843

1685. Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
(Submitter supplied) Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
5 related Platforms 13 Samples
FTP download: GEO (JSON, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119428/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489248
Series		Accession: GSE119428	ID: 200119428

1686. Human Adipocytes Regulate Gene Expression in Triple-negative Breast Cancer Assessed by NGS  Sequencing
(Submitter supplied) Adipocyte was found play a pivotal role in tumorgenesis, progression and metastasis in breast cancer. However, affection of adipocyte on gene expression profile in triple-negative breast cancer (TNBC) is still not clear. In the present study, firstly we reported the gene expression profiles of TNBC regulated by human adipocytes using NGS. TNBC cell MDA-MB-231 was used in this study. MDA-MB-231 cells were treated with medium derived from adipocytes culture supernatants. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA489010
Series		Accession: GSE119377	ID: 200119377

1687. HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108151/
Series		Accession: GSE108151	ID: 200108151

1688. HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells [Bru-seq]
(Submitter supplied) The biological properties of pancreatic cancer stem cells (PCSCs) remain incompletely defined and the central regulators are unknown. By bioinformatic analysis of a PCSC-enriched gene signature, we identified the transcription factor HNF1A as a putative central regulator of PCSC function. Levels of HNF1A and its target genes were found to be elevated in PCSCs and tumorspheres, and depletion of HNF1A resulted in growth inhibition, apoptosis, impaired tumorsphere formation, PCSC depletion, and downregulation of OCT4 expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108149/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422593
Series		Accession: GSE108149	ID: 200108149

1689. Expression profiling of NRAS knockout in embryonal rhabdomyosarcoma (ERMS) cells
(Submitter supplied) Targeted disruption of NRAS was performed in a stable 381T ERMS cell line harboring tamoxifen inducible CRISPR/Cas9 gRNA against NRAS
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118939/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487363
Series		Accession: GSE118939	ID: 200118939

1690. Pharmacologic inhibition of STAT5 in AML
(Submitter supplied) The transcription factors STAT5A and STAT5B are essential downstream mediators of many tyrosine kinases, particularly in hematopoietic cancers. As such, STAT5 is activated by FLT3-ITD, which is a constitutively active tyrosine kinase driving the pathogenesis of acute myeloid leukemia (AML). Since STAT5 is a critical mediator of diverse malignant properties of AML cells, direct targeting of STAT5 function is of significant clinical value. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401761
Series		Accession: GSE103510	ID: 200103510

1691. Oncogenic Serine-Threonine Kinase Receptor Associated Protein Supports Hepatocellular Carcinoma Cell Growth by Enhancing Wnt/β-catenin Signaling
(Submitter supplied) Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and lung cancers, promoting their growth. We identify the upregulation of STRAP in hepatocellular carcinomas. Elevated STRAP endows tumor cells with growth advantage by reprograming a variety of metabolic processes and signaling pathways critical for hepatocellular carcinoma progression. Especially, enhanced Wnt/β-catenin signaling is likely to be a major effector of its tumor-promoting role.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101061/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393645
Series		Accession: GSE101061	ID: 200101061

1692. scRNAseq reveals mechanisms of Merkel cell carcinoma acquired immunotherapy resistance [2]
(Submitter supplied) PBMC and tumor specimen from a Merkel cell carcinoma tumor at time of immunotherapy resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24676 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484204
Series		Accession: GSE118056	ID: 200118056

1693. scRNAseq reveals mechanisms of Merkel cell carcinoma acquired immunotherapy resistance [1]
(Submitter supplied) Serial blood draws from a single patient and serial tumor biopsies from the same patient  with metastatic Merkel cell polyomavirus Merkel cell carcinoma, who was treated with cellular immunotherapy targeting MCPyV (autologous endogenous T cell therapy) followed by checkpoint inhibitors (anti-PD1 and anti-CTLA4).  The patient had a 22 month clinical response followed by late/acquired resistance.  We performed scRNAseq using the 10x genomics 3' Chromium expression assay to determine potential mechanisms contributing to immunotherapy response and late resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483959
Series		Accession: GSE117988	ID: 200117988

1694. Communication of prostate cancer cells with bone cells via extracellular vesicle RNA; a potential mechanism of metastasis
(Submitter supplied) Analysis of miRNA and mRNA within extracellular vesicles obtained from prostate cancer PC3 cells. Kaighn ME, et al. Establishment and characterization of a human prostatic carcinoma cell line (PC-3). Invest. Urol. 17: 16-23, 1979. PubMed: 447482
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483056
Series		Accession: GSE117744	ID: 200117744

1695. The BCL-2 Inhibitor Venetoclax in Combination with Azacitidine Disrupts Energy Metabolism and Targets Leukemia Stem Cells in Acute Myeloid Leukemia Patients
(Submitter supplied) The manuscript summarizes clinical and laboratory-based evaluation of 33 AML patients treated with a novel drug combination, venetoclax and azacytidine. Our findings indicate that this regimen is exceptionally promising for the treatment of de novo AML patients. The improvement in outcomes in comparison to conventional therapy is quite remarkable. The manuscript explores the mechanistic basis for the clinical outcomes, testing the hypothesis that venetoclax and azacytidine effectively target leukemia stem cells (LSCs) in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA479415
Series		Accession: GSE116567	ID: 200116567

1696. Global identification of Androgen Receptor and EGR1 binding sites in melanoma reveals enriched co-binding at genes regulated by the lncRNA SLNCR
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 11 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116191/
Series		Accession: GSE116191	ID: 200116191

1697. Transcriptional profiling of WM1976 cells with siRNA knockdown of the long non-coding RNA SLNCR
(Submitter supplied) RNA-Seq was used to profile transcriptional changes induced by siRNA knockdown of the long non-coding RNA SLNCR (all isoforms).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116188/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477661
Series		Accession: GSE116188	ID: 200116188

1698. Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by genome tiling array; Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL21145 GPL16686 GPL16791 11 Samples
FTP download: GEO (BED, CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113372/
Series		Accession: GSE113372	ID: 200113372

1699. Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements [Whole RNA-Seq]
(Submitter supplied) We empirically assess the measurement precision and sensitivity of a suite of gene expression technologies via a consensus modelling method called the row-linear model.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113371/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450941
Series		Accession: GSE113371	ID: 200113371

1700. Perivascular signals alter global genomic profile of glioblastoma and response to temozolomide in a gelatin hydrogel
(Submitter supplied) Glioblastoma (GBM) is the most common primary malignant brain tumor, with patients exhibiting poor survival (median survival time: 15 months). Difficulties in treating GBM include not only the inability to resect the diffusively-invading tumor cells but also therapeutic resistance. The perivascular niche within the GBM tumor microenvironment contributes significantly to tumor cell invasion, cancer stem cell maintenance, and has been shown to protect tumor cells from radiation and chemotherapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111231/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436235
Series		Accession: GSE111231	ID: 200111231

1701. Replicated transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]
(Submitter supplied) To identify differentially expressed transcripts  in Cancer and Normal Prostate cells global transcript abundance was assayed by replicated (n=3) stranded RNA-Sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70466/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA288751
Series		Accession: GSE70466	ID: 200070466

1702. Transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]
(Submitter supplied) To identify differentially expressed transcripts (both annotated and unannotated) in Cancer and Normal Prostate cells global transcript abundance was assayed by RNA-Sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 2 Samples
FTP download: GEO (CSV, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62818/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA265213
Series		Accession: GSE62818	ID: 200062818

1703. Transcriptome profiling of Normal and Cancerous Prostate Cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by RT-PCR; Expression profiling by high throughput sequencing
6 related Platforms 24 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62410/
Series		Accession: GSE62410	ID: 200062410

1704. Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma
(Submitter supplied) A methionine substitution at lysine 27 on histone H3 variants (H3K27M) characterizes ~80% of diffuse intrinsic pontine gliomas (DIPG) and inhibits PRC2 in a dominant negative fashion. Yet, the mechanisms for this inhibition and abnormal epigenomic landscape have not been resolved. Using quantitative proteomics, we discovered that robust PRC2 inhibition requires levels of H3K27M greatly exceeding those of PRC2, seen in DIPG. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 64 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118954/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487522
Series		Accession: GSE118954	ID: 200118954

1705. Spatially Constrained Tandem Bromodomain Inhibition Bolsters Sustained Repression of BRD4 Transcriptional Activity for TNBC Cell Growth
(Submitter supplied) We performed RNA-seq of MDA-MB-231 cells that were treated with MS645 or JQ1 at 50 nM and 500 nM in an effort to understand how MS645 exerts such a profound cell growth inhibition on cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115550/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475425
Series		Accession: GSE115550	ID: 200115550

1706. Short-term effect of Boost versus Radical doses of Intraoperative electron Radiotherapy in breast cancer tumor bed using high-throughput approaches
(Submitter supplied) Importance: Intra-operative electron Radiation Therapy as a partial-breast single high dose radiotherapy, leads to decrease the local recurrence through tumor bed modification. Objective: This study designed to investigate short-term effect of the dose- dependent and -independent molecular mechanisms and biological pathway of tumor bed modification induced by Intra-operative electron Radiation Methods: Six random selected breast cancer patients entered into our study and all patients by referee to their pathological report were treated by doses of 12Gy as a Boost dose and 21Gy as a Radical dose and the samples were categorized into three groups which included: Margin Before irradiation, Margin After immediately irradiation and Margin 24 hours After irradiation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119204/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488462
Series		Accession: GSE119204	ID: 200119204

1707. RNA-Seq analysis of long-term estrogen-deprived (LTED) MDA-MB-134VI (MM134) and SUM44PE (SUM44) ILC cell lines
(Submitter supplied) Background: Invasive lobular breast carcinoma (ILC) is a histological subtype of breast cancer that is characterized by loss of E-cadherin, and high expression of estrogen receptor alpha (ER). Many patients with ILC are effectively treated with adjuvant aromatase inhibitors (AIs), however, acquired AI resistance remains a significant problem. Methods: To identify underlying mechanisms of acquired antiestrogen resistance in ILC, we developed a total of 6 long-term estrogen-deprived (LTED) variant cell lines of the human ILC cell lines SUM44PE (SUM44; 2 lines) and MDA-MB-134VI (MM134; 4 lines). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480032
Series		Accession: GSE116744	ID: 200116744

1708. RNA-sequencing of tamoxifen-resistant and -sensitive breast cancer cell lines.
(Submitter supplied) We performed RNA-sequencing on 7 tamoxifen-resistant (MCF-7 Tam1, T-47D Tam1, T-47D Tam2, ZR-75-1 Tam1, ZR-75-1 Tam2, BT474 Tam1 and BT-474 Tam2) and their isogenic parental (MCF-7, T-47D, ZR-75-1 and BT-474) breast cancer cell lines. The tamoxifen-resistant cell lines were generated from the parentel cell lines by continuous administration of 1 µM 4-OH-tamoxifen for eight to twelve months. RNA- sequencing was performed to determine the changes in the expression of genes in the resistant clones as well as pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111151/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436018
Series		Accession: GSE111151	ID: 200111151

1709. Transcriptomic Reprogramming of Prostate Cancer Cells Driven by Stroma-Derived SPINK1
(Submitter supplied) Recent advances in next generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways and responses. We performed this study to investigate the transcriptome profiling (RNA-seq) of prostate cancer cells upon in vitro treatment with the conditioned media from prostate stromal cells exogenously expressing human SPINK1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427589
Series		Accession: GSE108545	ID: 200108545

1710. Polycomb complexes associate with enhancers to promote oncogenic transcriptional programs in cancer
(Submitter supplied) The Polycomb repressive complexes PRC1 and PRC2 play an essential role in cell fate decisions, embryonic development and gene regulation. While the functions of PRC2 in cancer are under intense study, the function of PRC1 in cancer remains largely unexplored. Here, we show that RNF2, the gene encoding RING1B, and canonical PRC1 (cPRC1) genes are amplified and overexpressed in breast cancer. Specifically, in estrogen receptor positive (ER+) breast cancer cells, cPRC1 is functionally associated with enhancers and genes regulated by ERa, while in triple negative breast cancer (TNBC) cells, a different cPRC1 variant is recruited to enhancers and promoters occupied by the bromodomain protein BRD4. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 57 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107176/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419210
Series		Accession: GSE107176	ID: 200107176

1711. RNA-Seq analysis to identify novel genes associated with Neuropilin-1 expression in the BT-474 breast cancer cell model
(Submitter supplied) Background: Neuropilin-1 (NRP-1) is a non-tyrosine kinase glycoprotein receptor that elicits multiple functions depending on the ligand bound. It is known to promote cancer progression however; transcriptome-wide changes triggered by NRP-1 are not defined. In this study we aimed to identify novel molecules associated with NRP-1 expression using a global transcriptomic approach in a recombinant breast cancer cell model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106638/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417487
Series		Accession: GSE106638	ID: 200106638

1712. Effect of PDZ domain binding Kinase inhibition using TOPK-32 (called PBKi) on C4-2 cell transcriptome
(Submitter supplied) Analysis of C4-2 prostate cancer cell line after 6 hrs of treatment with TOPK-32. PBK is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of PBK in prostate carcinogenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64341/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270770
Series		Accession: GSE64341	ID: 200064341

1713. Effect of PBK knockdown on C4-2 cell transcriptome
(Submitter supplied) Analysis of C4-2 Prostate cancer cell line after 72 hours of knockdown. PBK is overexpressed in a number of solid tumours, including prostate cancer. Results provide insight into the molecular mechanisms of PBK in prostate carcinogenesis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63701/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA268829
Series		Accession: GSE63701	ID: 200063701

1714. Gene expression of DBTRG-05MG treated with dbcAMP or miR-1275 mimics
(Submitter supplied) Samples 1-5 were the microRNA-seq data of DBTRG-05MG treated with dbcAMP at 0/6/12/24/48 hours. Sample 6-17 were the analysis of DBTRG-05MG cells treated with control-media, dbcAMP, miR-1275 mimics and combined dbcAMP and miR-1275 mimics on day3.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL23227 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119161/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488284
Series		Accession: GSE119161	ID: 200119161

1715. Comparing oestrogen-responsive genes in endometrial and breast cancer cell lines
(Submitter supplied) Up to 80% of endometrial and breast cancers express the oestrogen receptor ERa. Unlike breast cancer, anti-oestrogen therapy has had limited success in endometrial cancer, raising the possibility that oestrogen has different effects in the two cancer types. We investigated the role of oestrogen in endometrial and breast cancers using cell lines and found that oestrogen-responsive genes were predominantly unique between the two cancer types.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421096
Series		Accession: GSE107693	ID: 200107693

1716. Aberrant expression of CITED2 promotes prostate cancer metastasis by activating the nuceolin-AKT pathway.
(Submitter supplied) We found that CITED2 is highly expressed in metastatic prostate cancer, and its expression is correlated with poor survival in pateints. In this study, we used an siRNA to decrease CITED2 expression in PC3 cells. A RNA-seq approach was utilized in order to determine global gene expression changes  in CITED2 knockdown cells compared to control cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119113/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA488188
Series		Accession: GSE119113	ID: 200119113

1717. Discovery of a Pro-Tumoral Clonogenic Unipotent Neutrophil Progenitor in Mouse and Human Bone Marrow
(Submitter supplied) Neutrophils are short-lived immune cells that play important roles in a variety of diseases. The oligopotent Granulocyte Monocyte Progenitors (GMP) in the bone marrow give rise to monocytes and all granulocytes. Although several monocyte progenitors have been identified in mouse bone marrow, the unipotent neutrophil progenitors are still not well-defined. Here, we use Cytometry by Time-of-Flight (CyTOF) and Single-cell RNA-Sequencing (scRNA-Seq) methodologies to identify a committed unipotent early-stage neutrophil progenitor in adult mouse bone marrow. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481252
Series		Accession: GSE117131	ID: 200117131

1718. Androgen receptor functions as transcriptional repressor of Cancer Associated Fibroblast (CAF) activation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107321/
Series		Accession: GSE107321	ID: 200107321

1719. Androgen receptor functions as transcriptional repressor of Cancer Associated Fibroblast (CAF) activation [RNA-seq]
(Submitter supplied) The age-associated increase of cancer risk has been linked with stromal fibroblast senescence and early steps of Cancer Associated Fibroblast (CAF) activation. Surprisingly little is known about the role of androgen receptor (AR) signalling in this context. We show that AR expression is down-modulated in stromal fibroblasts underlying premalignant skin cancer lesions (actinic keratoses, AK) as well as in CAFs from the three major skin cancer types, squamous (SCC) and basal cell (BCC) carcinomas and melanomas. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107319/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419758
Series		Accession: GSE107319	ID: 200107319

1720. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability [CLIP-seq]
(Submitter supplied) Thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome, but specific biological functions and biochemical mechanisms have been discovered for only about a dozen lncRNAs. One specific lncRNA, Non-coding RNA Activated by DNA Damage (NORAD), has recently been shown by genetic deletion to be required for maintaining genomic stability, but its molecular mechanism is unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115429/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474942
Series		Accession: GSE115429	ID: 200115429

1721. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 26 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114953/
Series		Accession: GSE114953	ID: 200114953

1722. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability [RNA-seq]
(Submitter supplied) Thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome, but specific biological functions and biochemical mechanisms have been discovered for only about a dozen lncRNAs. One specific lncRNA, Non-coding RNA Activated by DNA Damage (NORAD), has recently been shown by genetic deletion to be required for maintaining genomic stability, but its molecular mechanism is unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114946/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473320
Series		Accession: GSE114946	ID: 200114946

1723. sgRNA cassette sequencing and RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111635/
Series		Accession: GSE111635	ID: 200111635

1724. Poly(A)+ RNA-seq from H226 cells expressing doxycycline-inducible Control (non-targeting) and p63-targeting shRNAs
(Submitter supplied) To determine the impact of ΔNp63α knockdown on steady-state mRNA levels, we performed poly(A)-enriched RNA-seq analysis of lung squamous cell carcinoma line H226 (inducible shControl and shp63) in the presence of 1µg/mL doxycycline to induce shRNA expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111619/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437576
Series		Accession: GSE111619	ID: 200111619

1725. A novel long non-coding RNA HOXC-AS3 mediates tumorigenesis of gastric cancer by binding to YBX1
(Submitter supplied) Recently, increasing evidence shows that long noncoding RNAs (lncRNAs) play a significant role in human tumorigenesis. However, the function of lncRNAs in human gastric cancer remains largely unknown.  By using publicly available expression profiling data from gastric cancer and integrating bioinformatics analyses, we screen and identify a novel lncRNA, HOXC-AS3. HOXC-AS3 is significantly increased in gastric cancer tissues and is correlated with clinical outcomes of gastric cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119021/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487783
Series		Accession: GSE119021	ID: 200119021

1726. Neural progenitors derived from Tuberous Sclerosis Complex patients exhibit attenuated PI3K/AKT signaling and delayed neuronal differentiation
(Submitter supplied) Tuberous Sclerosis Complex (TSC) is a disease caused by autosomal dominant mutations in the TSC1 or TSC2 genes, and is characterized by tumor susceptibility, brain lesions, seizures and behavioral impairments. The TSC1 and TSC2 genes encode proteins forming a complex (TSC), which is a major regulator and suppressor of mammalian target of rapamycin (mTOR) in complex 1 (mTORC1), a signaling complex that promotes cell growth and proliferation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111584/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437467
Series		Accession: GSE111584	ID: 200111584

1727. Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (shRNA targeting)
(Submitter supplied) Differentiation events contribute to cellular heterogeneity within tumors and influence disease progression and response to therapy. Here we dissect the mechanisms controlling intratumoral heterogeneity within basal-like breast cancers. We show that cancer cells can transition between a differentiation state related to that of normal luminal progenitors and a state closer to that of mature luminal cells, and that this occurs through asymmetric cell divisions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84143/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328143
Series		Accession: GSE84143	ID: 200084143

1728. Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (Expression profiles)
(Submitter supplied) Differentiation events contribute to cellular heterogeneity within tumors and influence disease progression and response to therapy. Here we dissect the mechanisms controlling intratumoral heterogeneity within basal-like breast cancers. We show that cancer cells can transition between a differentiation state related to that of normal luminal progenitors and a state closer to that of mature luminal cells, and that this occurs through asymmetric cell divisions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84080/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327998
Series		Accession: GSE84080	ID: 200084080

1729. Effect for target mRNA degradation by methylated microRNAs
(Submitter supplied) To confirme the function of methylated micro RNAs (miR-17 and let-7a), we transfected methylated or non-methylated microRNAs to DICER KO HCT116 cell line. mRNA were isolated at 48 houes after transfection. This data show that the function were different between methylated or non-methylated microRNAs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE119nnn/GSE119013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA487774
Series		Accession: GSE119013	ID: 200119013

1730. Regulation of cellular heterogeneity and rates of symmetric and asymmetric divisions in triple-negative breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84149/
Series		Accession: GSE84149	ID: 200084149

1731. Non-inflammatory tumor microenvironment of Diffuse Intrinsic Pontine Glioma (DIPG)
(Submitter supplied) Diffuse intrinsic pontine glioma (DIPG) is a universally fatal malignancy of the childhood central nervous system, with a median overall survival of 9-11 months. We have previously shown that primary DIPG tissue contains numerous tumor-associated macrophages, and substantial work has demonstrated a significant pathological role for adult glioma-associated macrophages. However, work over the past decade has highlighted many molecular and genomic differences between pediatric and adult glioblastomas (GBM). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474825
Series		Accession: GSE115397	ID: 200115397

1732. Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response
(Submitter supplied) Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essentialness and functions of HNRNPC in tumors were not clear. We showed that repression of HNRNPC in the breast cancer cells MCF7 and T47D inhibited cell proliferation and tumor growth. Our computational inference of the key pathways and extensive experimental investigations revealed that the cascade of interferon responses mediated by RIG-I was responsible for such tumor-inhibitory effect. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20795 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100451/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391829
Series		Accession: GSE100451	ID: 200100451

1733. RNA sequencing of lncRNAs knockdown in human pancreatic cancer cell lines
(Submitter supplied) We report the transcriptome changes that result from the transient knockdown of FAM83H-AS1 in Aspc1 cells and transient knockdown of LINC00673 in Panc1 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (CSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96931/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380131
Series		Accession: GSE96931	ID: 200096931

1734. Single-cell analysis reveals stochastic regulation of type I IFN production by plasmacytoid dendritic cells and identifies host-derived environmental cues as amplifier of type I IFN production
(Submitter supplied) Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mech-anisms that control this process are poorly understood. Here, we developed a droplet-based microfluidic platform and investigated type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNF alpha production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (CSV, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114161/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474920
Series		Accession: GSE114161	ID: 200114161

1735. PRMT2 links histone H3R8 asymmetric dimethylation to oncogenic activation and tumorigenesis of glioblastoma
(Submitter supplied) Here we show that PRMT2 is highly expressed in GBM, which is correlated with poor prognosis. The silencing of PRMT2 inhibits GBM cell growth and glioblastoma stem cell self-renewal in vitro and suppreses orthotopic tumor growth. Transcriptome analysis demonstrated that PRMT2 depletion leads to significant deregulation of genes mainly associated with cell cycle progression and pathways in cancer. In agreement with previously published results, we show that PRMT2 is responsible for H3R8 asymmetric methylation (H3R8me2a) and that H3R8me2a enrichment at promoters and enhancers is closely correlated with known active histone marks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL23227 GPL20301 19 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110424/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433671
Series		Accession: GSE110424	ID: 200110424

1736. Chromatin de-condensation by switching substrate elasticity
(Submitter supplied) The mortality in cancer is mostly related to the development of metastases that colonize and comprise the function of vital organs. During the process of dissemination to form metastases, tumor cells face changing environments. Although the consequences of the changes in chemical environment have widely been investigated, much less is known about the effects of the physical changes. We have developed a culture model in which human colon cancer cells have been recurrently grown on soft substrates versus standard rigid substrates. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106166/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415803
Series		Accession: GSE106166	ID: 200106166

1737. Transcriptome profiles of POM121-knockout prostate cancer cell lines
(Submitter supplied) Nucleoporins are major constituents of nuclear pore complexes, molecular conglomerates embedded within the nuclear envelope that participate in bidirectional trafficking between nucleus and cytoplasm, chromatin silencing and organization, and transcriptional regulation . This functional vantage point is of utmost importance for fundamental cell processes such as intracellular signaling, cell migration, DNA repair and cell division, all of which can be impaired when the molecular identity of the NE and nuclear pore complex is compromised, as seen in cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103637/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA403831
Series		Accession: GSE103637	ID: 200103637

1738. RNAseq data from SCCOHT1 and OVCAR8 ovarian cancer cells treated with BET inhibitors
(Submitter supplied) The antitumor activity of bromodomain inhibitors (BETi) has been demonstrated across numerous types of cancer. As such, these inhibitors are currently undergoing widespread clinical evaluation. However, predictive biomarkers allowing the stratification of tumors into responders and non-responders to BETi are lacking. Here, we show significant anti-proliferative effects of BETi in vitro and in vivo against aggressive SCCOHT1 ovarian cancer models lacking the SWI/SNF-related, SMARCA4 protein . more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102908/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399251
Series		Accession: GSE102908	ID: 200102908

1739. A Novel Class of MicroRNA Recognition Elements That Function Only in Open Reading Frames
(Submitter supplied) MicroRNA (miRNA) are well known to target 3’ untranslated regions (3’UTR) in mRNAs to silence gene expression at post-transcriptional levels. Multiple reports have also indicated the capability of miRNAs to target protein-coding sequences (CDS); however, miRNAs have been generally believed to function in a similar mechanism(s) regardless of the location of their action sites. We herein report a class of miRNA recognition elements (MREs) that exclusively function in CDS regions in humans. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL20795 GPL16791 18 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115146/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473925
Series		Accession: GSE115146	ID: 200115146

1740. Primary T cells from cutaneous T-cell lymphoma skin explants display an exhausted  immune checkpoint profile
(Submitter supplied) Cutaneous T-cell lymphoma (CTCL) develops from clonally expanded CD4+ T cells in a  background of chronic inflammation. Dendritic cells (DCs) are potent T-cell stimulators; yet  despite DCs’ extensive presence in skin, cutaneous T cells in CTCL do not respond with  effective anti-tumor immunity. We evaluated primary T-cell and DC émigrés from epidermal and  dermal explant cultures of skin biopsies from CTCL patients (n = 37) and healthy donors (n = 5). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 52 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113113/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450035
Series		Accession: GSE113113	ID: 200113113

1741. A novel transcriptional network for the Androgen Receptor in human epididymis epithelial cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109063/
Series		Accession: GSE109063	ID: 200109063

1742. A novel transcriptional network for the Androgen Receptor in human epididymis epithelial cells [RNA-Seq]
(Submitter supplied) The androgen receptor (AR) has a pivotal role in regulating gene expression in the male reproductive system. Due to the involvement of AR in prostate cancer, its role is best studied in the prostate gland epithelium and prostate cancer cell lines. Here we investigate the transcriptional program of AR in normal human epididymis epithelial (HEE) cells. After AR stimulation of caput HEE cells with the synthetic androgen R1881, AR targets were revealed with RNA-sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109062/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429557
Series		Accession: GSE109062	ID: 200109062

1743. RHBDF2 in Stromal Fibroblasts Mediates TGF-b Signal and Enhances Cancer Cell Invasion via Intercellular Cross-Talk
(Submitter supplied) Cancer-associated fibroblasts (CAFs) existing in tumor stroma play a crucial role in tumor progression. Here, we show that stromal fibroblasts near cancer cells are likely to display up-regulated RHBDF2 expression caused by chronic stimulation from pro-inflammatory cytokines. RHBDF2 promotes both the cleavage of type I transforming growth factor (TGF)-b receptor, through tumor necrosis factor α converting enzyme activation, and the motility of CAFs upon stimulation with TGF-b1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327180
Series		Accession: GSE83834	ID: 200083834

1744. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 13 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118767/
Series		Accession: GSE118767	ID: 200118767

1745. Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma
(Submitter supplied) Immune checkpoint blockade (ICB) therapy provides remarkable clinical gains, where melanoma is at the forefront of its success. However, only a subset of patients with advanced tumors currently benefit from these therapies, which at times incur considerable side-effects and costs. Constructing such predictors of patient’s response has remained a serious challenge due to the complexity of the immune response and the shortage of large ICB-treated patient cohorts including both omics and response data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 37 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115821/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476140
Series		Accession: GSE115821	ID: 200115821

1746. Sequencing facilitates quantitative analysis of transcriptomes in wild type and Lrp6-knockdown cells
(Submitter supplied) Purpose: The goals of this study are to determine the LRP6-mediated splicing regulation, and cellular transcriptomes from rat and human are analysised by deep sequencing. Methods: The mRNA profiles of WT and LRP6 KD were generated by deep sequencing, using Illumina HiSeq 4000. And the transcript isoform difference betwwen the two group were analysied by bioinformation, Semiquantitative PCR was performed to identify the analysis result. more...
Organism:	Homo sapiens; Rattus norvegicus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL22396 GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399100
Series		Accession: GSE102770	ID: 200102770

1747. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (RNAmix_CEL-seq2 )
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 1 Sample
FTP download: GEO (CSV, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117617/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482659
Series		Accession: GSE117617	ID: 200117617

1748. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (9 cell mixture dataset).
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117450/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482132
Series		Accession: GSE117450	ID: 200117450

1749. Comparison of transcriptional changes after CD28/CD3z and 4-1BB/CD3z chimeric antigen receptor ligation
(Submitter supplied) The adoptive transfer of chimeric antigen receptor- (CAR) modified T cells is revolutionizing the treatment of B cell malignancies and has the potential to be applied to other diseases. CARs redirect T cell specificity by linking an antigen recognition domain to T cell signaling modules comprised of CD3z to provide signal 1, and CD28 or 4-1BB to provide costimulation. CD28/CD3z and 4-1BB/CD3z CARs confer differences in effector function and cell fate that affect clinical efficacy and toxicity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109161/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429804
Series		Accession: GSE109161	ID: 200109161

1750. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Drop-Seq)
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 1 Sample
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118706/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486516
Series		Accession: GSE118706	ID: 200118706

1751. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Cel_Seq)
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 1 Sample
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118704/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486514
Series		Accession: GSE118704	ID: 200118704

1752. AmpliSeq Transcriptome Analysis of cells stimulated with polyIC in presence of GFP or NS5 protein
(Submitter supplied) We compared polyIC stimulated cells in the presence of either GFP or NS5 protein
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23934 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118686/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486456
Series		Accession: GSE118686	ID: 200118686

1753. SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signaling
(Submitter supplied) Through integrated transcriptomic, epigenomic and proteomic analyses, we identified IGFBP2, an insulin growth factor (IGF) binding protein, as a direct SIRT6 target gene. We further show that SIRT6 haploinsufficiency, but not complete knock out of SIRT6 promotes IGFBP2 expression via increased H3K56 acetylation at the IGFBP2 locus allowing melanoma cell survival in the presence of MAPK signaling inhibitors (MAPKi). 
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 40 Samples
FTP download: GEO (BW, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102813/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399101
Series		Accession: GSE102813	ID: 200102813

1754. Next Generation Sequencing of ovarian CA-MSC & MSC Transcriptomes
(Submitter supplied) Carcinoma-associated mesenchymal stem cells (CA-MSCs) are critical stromal progenitor cells within the tumor microenvironment. We previously demonstrated that CA-MSCs differentially express BMP genes,  promote tumor cell growth,  increase cancer ‘stemness’ and  chemotherapy resistance. Here we use RNA sequencing of normal omental MSCs and ovarian CA-MSCs to demonstrate CA-MSCs have global changes in gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA486272
Series		Accession: GSE118624	ID: 200118624

1755. Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL18573 36 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111337/
Series		Accession: GSE111337	ID: 200111337

1756. Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [RNA-seq]
(Submitter supplied) Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, a higher primate-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111332/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436643
Series		Accession: GSE111332	ID: 200111332

1757. Plasma transcriptome profiling in patients with chronic kidney disease and end-stage renal disease
(Submitter supplied) Cardiovascular disease is the major cause of morbidity and death in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). Patients with CKD and ESRD are at high risk for myocardial dysfunction, ischemia and heart failure. The mechanisms linking impaired renal function and increased risk for cardiovascular diseases, however, remain elusive. In addition, conventional therapeutics proven effective in reducing cardiovascular events in general population fail to provide similar benefits in uremic patients. more...
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL17303 159 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97709/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382706
Series		Accession: GSE97709	ID: 200097709

1758. CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops
(Submitter supplied) Background: Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer. Results: We generated genome-wide regulatory element maps and performed genome-wide chromosome confirmation capture assays (in situ Hi-C) in normal and tumorigenic prostate cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL9052 GPL21290 GPL11154 32 Samples
FTP download: GEO (BED, GFF, NARROWPEAK, TAB, TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118514/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485892
Series		Accession: GSE118514	ID: 200118514

1759. Uridilation by TUT4/7 restricts retrotransposition of human Line-1s
(Submitter supplied) Purpose: the goal of this study was to test whether the amounts of genome-encoded Line-1s are influenced by TUTases and Mov10 Methods: RNA-Seq data were obtained for PA-1 or Hek293 Flp-IN T-Rex cells in which wild-type or mutant TUTases or Mov10 were overexpressed or the proteins were depleted by RNA interference Results: Minor changes (less than 0.4-fold) were observed in the amounts of mRNAs of Homo sapiens-specific Line-1 families in Hek293 Flp-IN T-Rex and PA-1 either overexpressing or depleted of TUTases and Mov10
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 49 Samples
FTP download: GEO (GTF, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105264/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415171
Series		Accession: GSE105264	ID: 200105264

1760. Global loss of epigenetic and transcriptional fidility defines a subclass of cancer with immunotherapy resistance [RCC]
(Submitter supplied) We report that some cancers have extensive loss of epigenetic and transcriptional fidelity, characterized widespread spurious transcription and mRNA processing defects (Loss of transcriptional fidelity: LTF+). LTF impairs transcriptional elongation and imposes a highly specific molecular phenotype where pathways regulated by long genes, such as those involved in inflammatory response are consistently impaired in LTF+ tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102661/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398334
Series		Accession: GSE102661	ID: 200102661

1761. Expression profiling of four replicates of MCF-7 cells treated with 100nM TCDD
(Submitter supplied) The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that binds pollutants, therapeutic drugs and endogenous ligands.  The AHR is expressed in all breast cancer subtypes and it can switch the aggressiveness of breast cancer cells from low to high depending on the ligand that it binds.  Jagged 1 (JAG1) is a NOTCH receptor ligand that is overexpressed in basal-like breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98514/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385320
Series		Accession: GSE98514	ID: 200098514

1762. The Estrogen Receptor variants β2 and β5 Induce Stem Cell Characteristics and Chemotherapy Resistance in Prostate Cancer through activation of Hypoxic Signaling
(Submitter supplied) Chemotherapy resistant prostate cancer is a major clinical problem. When the prostate cancer has become androgen deprivation resistant, one of the few treatment regimens left is chemotherapy. There is a strong connection between a cancer’s stem cell like characteristics and drug resistance. By performing RNA-seq we observed several factors associated with stem cells being strongly up-regulated by the estrogen receptor β variants, β2 and β5. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118449/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485690
Series		Accession: GSE118449	ID: 200118449

1763. AmpliSeq Transcriptome Analysis of Human Prostate Cancer Cells With or Without Overt SRRM4 Expression
(Submitter supplied) Prostate adenocarcinoma (AdPC) cells can undergo lineage switching to neuroendocrine cells and develop into therapy-resistant neuroendocrine prostate cancer (NEPC). While genomic/epigenetic alterations are shown to induce neuroendocrine differentiation via an intermediate stem-like state, RNA splicing factor SRRM4 can transform AdPC cells into NEPC xenografts through a direct neuroendocrine transdifferentiation mechanism. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118104/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484414
Series		Accession: GSE118104	ID: 200118104

1764. RNA-seq and Hi-C sequencing of neutrophil-like cells migrated through large or small pores
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20795 18 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115634/
Series		Accession: GSE115634	ID: 200115634

1765. ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 40 Samples
FTP download: GEO (BED, BW, CEL, NARROWPEAK, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102807/
Series		Accession: GSE102807	ID: 200102807

1766. ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [RNA-seq]
(Submitter supplied) Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the putative tumor suppressor proteins PBRM1 (BAF180) and ARID2 (BAF200) that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). Here, we integrate RNA-seq, ARID2 and histone mark ChIP-seq, and ATAC-seq data to show that PBAF acts to enhance or repress gene expression depending on the genomic context. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102806/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400186
Series		Accession: GSE102806	ID: 200102806

1767. Genome wide expression change by SMURF1 knocking down in MCF-7 cells
(Submitter supplied) We aim to the investigate the role of SMURF1 in breast cancer progression. MCF-7 cells were used as the model and SMURF1 was silenced by siRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102653/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398272
Series		Accession: GSE102653	ID: 200102653

1768. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL9052 1539 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118390/
Series		Accession: GSE118390	ID: 200118390

1769. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq [RNA-Seq]
(Submitter supplied) Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conduct single-cell RNA- sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Intercellular heterogeneity of gene expression programs within each tumor was variable and largely correlated with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 1534 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118389/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485429
Series		Accession: GSE118389	ID: 200118389

1770. Retinoic acid suppresses MYB in adenoid cystic carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98008/
Series		Accession: GSE98008	ID: 200098008

1771. Retinoic acid suppresses MYB in adenoid cystic carcinoma [RNA-seq]
(Submitter supplied) Translocations that drive overexpression of the oncogenic transcription factor MYB are molecular hallmarks of adenoid cystic carcinoma (ACC), a malignant salivary gland tumor. Surgical resection, whenever possible, is the standard therapy for ACC, but there are no available therapeutic options available if surgery fails. Here we performed a chemical genetic screen using a zebrafish embryo culture system and identified retinoic acid agonists as potent suppressors of c-myb. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383655
Series		Accession: GSE98007	ID: 200098007

1772. Specific Oxylipins Enhance Vertebrate Hematopoiesis via the Receptor GPR132
(Submitter supplied) Epoxyeicosatrienoic acids (EETs) are endogenous lipid signaling molecules with cardioprotective and vasodilatory actions. We recently showed that exogenous addition of 11,12-EET enhances hematopoietic induction and engraftment in mice and zebrafish. EETs are known to signal via a G-protein coupled receptor(s), but no specific EET receptor has been identified. Identification of an EET receptor would enable genetic interrogation of the EET signaling pathway and perhaps clinical use of this molecule. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL9052 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113550/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451492
Series		Accession: GSE113550	ID: 200113550

1773. Cyclin D1 levels induces global transcriptional downregulation in malignant lymphoid cells and correlate with total RNA levels in mantle cell lymphoma cell lines
(Submitter supplied) Study of the transcriptional role of cyclin D1 in lymphoid tumor cells with cyclin D1 oncogenic overexpression. We perform global transcriptional analysis of four mantle cell lymphoma cell lines and we observed a correlation between the cyclin D1 levels and the transcriptional output. We confirmed our hypothesis using a lymphoblastic cell lines (JVM-13) cyclin D1 negative, where the overexpression of a mutant, more stable, form of cyclin D1 downregulated the transcriptome globally.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA485139
Series		Accession: GSE118301	ID: 200118301

1774. Cancer associated mRNAs regulated by the Helix Loop Helix motif of human EIF3A
(Submitter supplied) Improper regulation of translation initiation, a vital check-point of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) has been associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (DIFF, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118239/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484941
Series		Accession: GSE118239	ID: 200118239

1775. TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 38 Samples
FTP download: GEO (BEDGRAPH, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107023/
Series		Accession: GSE107023	ID: 200107023

1776. TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells [RNA-seq]
(Submitter supplied) We report the gene expression profiles of TRPS-depleted and YAP 5SA overexpressing breast cancer cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107010/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418848
Series		Accession: GSE107010	ID: 200107010

1777. Cytoplasmic NPM1 maintains the leukemic state through HOX expression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 47 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111180/
Series		Accession: GSE111180	ID: 200111180

1778. Cytoplasmic NPM1 maintains the leukemic state through HOX expression [RNA-seq]  
(Submitter supplied) NPM1 is the most frequently mutated gene in cytogenetically normal acute myeloid leukemia (AML). In AML cells, NPM1 mutations result in abnormal cytoplasmic localization of the mutant protein (NPM1c). NPM1 mutations are founding genetic lesions, however it is unknown whether NPM1c is required to maintain the leukemic state. Here, we show that loss of NPM1c from the cytoplasm, either through nuclear relocalization or targeted degradation, results in downregulation of homeobox (HOX) genes, and differentiation and cell growth arrest of AML cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 33 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111178/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436127
Series		Accession: GSE111178	ID: 200111178

1779. Single-cell RNA sequencing of circulating tumor cells in hepatocellular carcinoma
(Submitter supplied) The purpose of this experiment is to detect and characterize circulating tumor cells in single cell sequence data and characterize the other cell types in the blood.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107747/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421273
Series		Accession: GSE107747	ID: 200107747

1780. Nutritional control of protein translation
(Submitter supplied) Regulation of protein translation is a key feature of many biological processes. Global protein translation as well as translation at the codon level can be regulated by RNA modifications. These modifications are particularly enriched in tRNAs, where they represent an additional regulatory layer on top of the primary RNA sequence. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the gut microbiota and absorbed in the intestine. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102315/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397422
Series		Accession: GSE102315	ID: 200102315

1781. Global transcriptome analysis of HAP1 cells
(Submitter supplied) We analyzed the global change in transcription upon CHD3-KO and SENP1-KO compared to control HAP1 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111272/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436386
Series		Accession: GSE111272	ID: 200111272

1782. Next generation sequencing facilities quantitative analysis of negative control HCT116 cells and 5MP1-overexpressed HCT116 cells.
(Submitter supplied) To investigate the downstream targets of eIF5 mimic protein 1 (5MP1), also known as Basic Leucine Zipper and W2 domains 2 (BZW2; Ensembl:ENSG00000136261), we performed a transcriptomic analysis using high throoughput RNA sequencing (RNA-seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA484417
Series		Accession: GSE118105	ID: 200118105

1783. Identification of relationships between Molecular and Imaging Phenotypes in Non-small cell lung cancer using radiogenomics Map
(Submitter supplied) Purpose:  To create a radiogenomic map linking computed tomographic (CT) image features and gene expression profiles generated by RNA sequencing for patients with non-small cell lung cancer (NSCLC). Methods: A cohort of 113 patients with NSCLC diagnosed between April 2008 and September 2014 who had preoperative CT data and tumor tissue available was studied. For each tumor, a thoracic radiologist recorded 87 semantic image features, selected to reflect radiologic characteristics of nodule shape, margin, texture, tumor environment, and overall lung characteristics. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 130 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103584/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401995
Series		Accession: GSE103584	ID: 200103584

1784. Heat shock-induced ribosomal intergenic spacer RNA
(Submitter supplied) Cells adapt to environmental stressors such as heat shock and extracellular acidosis through formation of nuclear membrane-less compartments called Amyloid bodies (A-bodies). Stressors activate formation of Amyloid bodies (A-bodies) via induction of ribosomal intergenic spacer RNA (rIGSRNA). RNA-seq on non-ribosome depleted RNA from human MCF7 cells exposed to heat shock (43C, 30 minutes) revealed the heat shock-specific expression profile of rIGSRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115731/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475962
Series		Accession: GSE115731	ID: 200115731

1785. Effect of CRISPR-Cas9 mediated knock-out of integrin alpha2 on the transcriptome of DU145 prostate cancer cell grown as a spheroid culture
(Submitter supplied) CRISPR-cas9 technology was used to knock out alpha2 integrin in DU145 cells. To create two cell lines that could be compared to each other in an appropriate manner, these cells were transfected either with alpha2 integrin cDNA or empty vector. The objective of the study was to find potential alpha2 integrin regulated genes when the cells were grown as spheroids.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111507/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437244
Series		Accession: GSE111507	ID: 200111507

1786. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 50 Samples
FTP download: GEO (BROADPEAK, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110657/
Series		Accession: GSE110657	ID: 200110657

1787. Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. [RNA-seq]
(Submitter supplied) Chromosomal rearrangements resulting in the fusion of TMRPSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other ETS factors, including ETV1, ETV4, and ETV5. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110656/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434202
Series		Accession: GSE110656	ID: 200110656

1788. RNA-seq profiling of patient-derived xenograft models in Urothelial Cancer
(Submitter supplied) To probe the tissue source (cancer cell VS stromal cell) of gene expression in the mixed tumor samples, we took advantage of a set of Urothelial Cancer patient-derived xenograft (PDX) models given that the transcriptome in these models is a mixture of human RNA (derived from cancer cells) and mouse RNA (derived from stromal cells).
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platform: GPL22245 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477510
Series		Accession: GSE116159	ID: 200116159

1789. Genetic and transcriptional variation alters cancer cell line drug response
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114462/
Series		Accession: GSE114462	ID: 200114462

1790. Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]
(Submitter supplied) 10X Genomics single cell RNAseq of MCF7 cells treated with bortezomib. Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471582
Series		Accession: GSE114461	ID: 200114461

1791. Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain L]
(Submitter supplied) 10X Genomics single cell RNAseq of MCF7 cells Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114460/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471583
Series		Accession: GSE114460	ID: 200114460

1792. Genetic and transcriptional variation alters cancer cell line drug response [MCF7]
(Submitter supplied) 10X Genomics single cell RNAseq of MCF7 cells Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114459/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471584
Series		Accession: GSE114459	ID: 200114459

1793. Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT
(Submitter supplied) The epithelial-mesenchymal transition (EMT) is a fundamental developmental process that is abnormally activated in cancer metastasis. Dynamic changes in alternative splicing occur during EMT. ESRP1 and hnRNPM are splicing regulators that promote an epithelial splicing program and a mesenchymal splicing program, respectively. The functional relationships between these splicing factors in the genome-scale remain elusive. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112516/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448058
Series		Accession: GSE112516	ID: 200112516

1794. Targeting tumour re-wiring by triple blockade of mTORC1, epidermal growth factor and estrogen receptor signalling pathways in endocrine resistant breast cancer
(Submitter supplied) Our data supports the potential combination of inhibition of ERBB2/3 signalling with mTORC1 perturbation and endocrine therapy in patients who have relapsed on endocrine therapy and retain a functional ER.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112401/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA447437
Series		Accession: GSE112401	ID: 200112401

1795. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation [ChiP-Seq and RNA-Seq]
(Submitter supplied) The interplay between transcription factors and epigenetic writers like the DNA methyltransferases (DNMTs), and the role of this interplay in modulating gene expression, is being increasingly appreciated. We investigated the interplay between ZBTB24, a zinc-finger protein belonging to the BTB-POZ family of transcription factors, and the de novo DNA methyltransferase DNMT3B. Both factors, when mutated, cause Immunodeficiency, Centromere Instability, and Facial anomalies (ICF) syndrome, suggesting they are mechanistically linked in some way, but almost nothing is known about ZBTB24. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 26 Samples
FTP download: GEO (BED, GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111683/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438030
Series		Accession: GSE111683	ID: 200111683

1796. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa
(Submitter supplied) RNA-sequencing of RDEB SCC tumors and RDEB normal skin
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111582/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437465
Series		Accession: GSE111582	ID: 200111582

1797. RNAseq analyze global transcriptome of changes between siIRF3 and siYAP in Gastric cancer cells
(Submitter supplied) Purpose: To investigate the signal crosstalk between IRF3 and YAP, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of IRF3 or YAP in HGC-27 cells. Methods: Total RNA was extracted from HGC-27 cell after transfection with negative control siRNA (n.c.), IRF3 siRNA (siIRF3) or YAP siRNA (siYAP). Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102112/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396691
Series		Accession: GSE102112	ID: 200102112

1798. Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis (ChIP-seq, RNA-seq)
(Submitter supplied) It remains unclear how epigenetic modulators impact the tumorigenic potential of Myc. Here we show that the core subunits, including Dpy30, of the major H3K4 methyltransferase complexes are selectively upregulated in Burkitt lymphoma, and Dpy30 is important for efficient genomic binding of Myc. Dpy30 heterozygosity does not affect normal animal physiology, but significantly suppressed lymphomagenesis and reduced expression of a subset of key pro-survival genes when Myc is hyper-activated. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 22 Samples
FTP download: GEO (BW, TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101853/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395707
Series		Accession: GSE101853	ID: 200101853

1799. Linking prostate cancer cell AR heterogeneity to distinct castration and Enzalutamide responses
(Submitter supplied) Molecular mechanisms underlying resistance to androgen deprivation therapy (ADT) and, in particular, to antiandrogen Enzalutamide, in treating castration-resistant prostate cancer (CRPC), remain incompletely understood. Through screening >120 CRPC patient samples, we observed 3 expression patterns of androgen receptor (AR) protein: primarily nuclear (nuc-AR), mixed nuclear/cytoplasmic expression (nuc/cyto-AR), and low/no expression (AR-/lo). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88752/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348463
Series		Accession: GSE88752	ID: 200088752

1800. AKR1C3-mediated adipose androgen generation fuels an adverse metabolic phenotype in polycystic ovary syndrome (PCOS)
(Submitter supplied) RNA-seq samples used to support a study into understanding of the association between androgens and adipose tissue
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 53 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84958/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335816
Series		Accession: GSE84958	ID: 200084958

1801. CDK12 mediated transcriptional regulation in U2OS cells
(Submitter supplied) While activation of canonical NF-κB signaling through the IKK complex is well studied, few regulators of NIK-dependent non-canonical p52 nuclear translocation have been identified. We discovered a novel role for cyclin dependent kinase 12 (CDK12) in transcriptionally regulating the non-canonical NF-κB pathway. High-content phenotypic screening identified a novel compound, 919278, which inhibits lymphotoxin β receptor (LTβR)- and FN14-dependent p52 nuclear translocation, but not TNFα receptor (TNFR)-mediated, canonical NF-κB p65 nuclear translocation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 56 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454480
Series		Accession: GSE113926	ID: 200113926

1802. ZBTB24 is a transcriptional regulator that coordinates with DNMT3B to control DNA methylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by array
Platforms: GPL11154 GPL23976 GPL16791 33 Samples
FTP download: GEO (BED, GTF, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111689/
Series		Accession: GSE111689	ID: 200111689

1803. Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide
(Submitter supplied) We conjugated NCD38 with two different Py-Im polyamides and analyzed the regions epigenetically altered by parental NCD38 and the two conjugates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18460 GPL18573 38 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108265/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423010
Series		Accession: GSE108265	ID: 200108265

1804.  Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy 
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  Deep sequencing has revealed that epigenetic modifiers are the most mutated genes in acute myeloid leukemia (AML). Thus, elucidating epigenetic dysregulation in AML is crucial to understand disease mechanisms. Here, we demonstrate that Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in the Polycomb repressive complex 2 (PRC2) and that its loss elicits an altered epigenetic state underlying refractory AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 30 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98380/
Series		Accession: GSE98380	ID: 200098380

1805.  Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy [RNA-Seq]
(Submitter supplied) Deep sequencing has revealed that epigenetic modifiers are the most mutated genes in acute myeloid leukemia (AML). Thus, elucidating epigenetic dysregulation in AML is crucial to understand disease mechanisms. Here, we demonstrate that Metal Response Element Binding Transcription Factor 2/Polycomblike 2 (MTF2/PCL2) plays a fundamental role in the Polycomb repressive complex 2 (PRC2) and that its loss elicits an altered epigenetic state underlying refractory AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98343/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384957
Series		Accession: GSE98343	ID: 200098343

1806. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme
(Submitter supplied) The human genome encodes a variety of poorly understood RNA species that remain challenging to identify using existing genomic tools. We developed chromatin run-on and sequencing (ChRO-seq) to map the location of RNA polymerase using virtually any input sample, including samples with degraded RNA that are intractable to RNA-seq. We used ChRO-seq to map nascent transcription in primary human glioblastoma (GBM) brain tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117832/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483346
Series		Accession: GSE117832	ID: 200117832

1807. Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL24268 GPL18573 41 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106925/
Series		Accession: GSE106925	ID: 200106925

1808. Epigenome editing of microsatellite repeat enhancers reveals specific regulatory functions and tumor dependencies [NRO-Seq]
(Submitter supplied) Various types of repetitive sequences are dysregulated in cancer but their contributions to oncogenesis are yet to be determined. Here we combine nascent transcription profiling with epigenome editing to test the function of GGAA microsatellites in Ewing sarcoma, a pediatric bone cancer where the oncogenic fusion protein EWS-FLI1 induces chromatin features of active enhancers at this class of repeats. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106915/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418458
Series		Accession: GSE106915	ID: 200106915

1809. Cardiomyocyte stress-response gene modules regulate cardiac hypertrophy and failure
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 1192 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95143/
Series		Accession: GSE95143	ID: 200095143

1810. Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure (RNA-Seq)
(Submitter supplied) Pressure overload induces a transition from cardiac hypertrophy to heart failure, but its underlying mechanisms remain elusive. Here we reconstruct a trajectory of cardiomyocyte remodeling and clarify distinct cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure, by integrating single-cardiomyocyte transcriptome with cell morphology, epigenomic state and heart function. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 1190 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95140/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376181
Series		Accession: GSE95140	ID: 200095140

1811. Circular DNA tumor viruses make circular RNAs
(Submitter supplied) Epstein-Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) cause ~2% of all  human cancers. RNase R-resistant RNA sequencing revealed that both  gammaherpesviruses encode multiple, uniquely stable, circular RNAs (circRNA). EBV  abundantly expressed both exon-only and exon-intron circRNAs from the BART locus  (circBARTs) formed from a spliced BART transcript and excluding the EBV miRNA  region. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL20795 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483204
Series		Accession: GSE117798	ID: 200117798

1812. Activation of Wnt signaling promotes olaparib resistant ovarian cancer.
(Submitter supplied) Sequencing of olaparib-resistant PEO1 derivatives (C4, C5, C10 and C18) and parental PEO1 (P1 and P2) cells was performed in order to determine mechanisms of acquired resistance in the resistant cell lines. PEO1 parental cell lines were authenticated prior to sequencing. PEO1 parental were confirmed to be BRCA2-mutated (5139C>G). Olaparib PEO1 resistant cells were generated through a step-wise escalation of olaparib (10nM to 8uM olaparib). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117765/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA483130
Series		Accession: GSE117765	ID: 200117765

1813. Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma
(Submitter supplied) The intrinsic drivers of migration in glioblastoma (GBM) are poorly understood. To better capture the native molecular imprint of GBM and its developmental context, we isolate human stem cell populations from GBM (GSC) and germinal matrix tissues and map their chromatin accessibility via ATAC-seq. We uncover two distinct regulatory GSC signatures, a developmentally-shared/proliferative and a tumor-specific/migratory one in which TEAD1/4 motifs are uniquely overrepresented. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 31 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117685/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482999
Series		Accession: GSE117685	ID: 200117685

1814. Stage-specific transcriptome analysis during differentiation from pluripotency to glial restricted progenitor stages
(Submitter supplied) The goals of this study are to compare NGS-derived neural transcriptome profiling (RNA-seq) and to investigate involving transcription factors at each stages
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482846
Series		Accession: GSE117664	ID: 200117664

1815. An atlas of genetic variation for linking pathogen-induced cellular traits to human disease
(Submitter supplied) Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with disease. To facilitate moving from associations to disease mechanisms, we leveraged the role of pathogens in shaping human evolution with the Hi-HOST Phenome Project (H2P2): a catalog of cellular GWAS comprised of 79 phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance (p<5x10-8) for phenotypes ranging from pathogen replication to cytokine production. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116172/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477542
Series		Accession: GSE116172	ID: 200116172

1816. Precise and Predictable CRISPR Chromosomal Rearrangement Editing Reveals Principles of Cas9-mediated Nucleotide Insertion
(Submitter supplied) Chromosomal rearrangements including large DNA-fragment inversions, deletions, and duplications by Cas9 with paired sgRNAs are important to investigate structural genome variations and developmental gene regulation, but little is known about the underlying mechanism. Here we report that disrupting CtIP or FANCD2, which is thought to function in NHEJ, enhances precise DNA-fragment deletion. In addition, by analyzing the inserted nucleotides at the junctions of DNA-fragment deletions, inversions, duplications, and characterizing the cleaved products, we find that Cas9 endonucleolytically cleaves the noncomplementary strand with a flexible scissile profile upstream of -3 position of the PAM site in vivo and in vitro, generating overhanged DSB ends. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113698/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453692
Series		Accession: GSE113698	ID: 200113698

1817. Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (RNAmix_Sort-seq)
(Submitter supplied) Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 1 Sample
FTP download: GEO (CSV, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117618/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482660
Series		Accession: GSE117618	ID: 200117618

1818. RNA-seq of PC9 cells tolerant to gefitinib
(Submitter supplied) EGFR inhibitors (EGFRi) are effective against EGFR mutant lung cancers. The efficacy of these drugs however is mitigated by the outgrowth of resistant cells, most often driven by a secondary acquired mutation in EGFR, T790M. We recently demonstrated that T790M can arise de novo during treatment (Hata et al., Nature Medicine 2016); it follows that one potential therapeutic strategy to thwart resistance would be identifying and eliminating these cells (referred to as drug tolerant cells (DTCs)) prior to acquiring secondary mutations like T790M. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482642
Series		Accession: GSE117610	ID: 200117610

1819. PBMC Fixation and Processing for Chromium Single-Cell RNA Sequencing
(Submitter supplied) Background:  Interest in single-cell whole transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In almost all reported works, investigators have used live cells which represent several inconveniences and limitations. Some recent cell fixation methods did not work with most primary cells including immune cells. Methods:    The methanol-fixation and new processing method was introduced to preserve PBMCs for single-cell RNA sequencing (scRNA-Seq) analysis on 10X Chromium platform. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL21290 9 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112845/
Series		Accession: GSE112845	ID: 200112845

1820. RNA Sequencing analysis of different genetically characterized lung cancer cell lines
(Submitter supplied) We performed RNA sequencing to assess changes in gene expression in lung cancer cell lines with MET genetic alterations with or without co-occurrence of JAK2 inactivating mutations. Different treatments have been administrated to activate or inhibit selected pathways in order to define MET signature and IFNg (or JAK/STAT) signature.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109720/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431798
Series		Accession: GSE109720	ID: 200109720

1821. Acquisition of a side population fraction through downregulation of MSL3, ZNF691, VPS45, ITGB3BP, TLE2, and ZNF498 augments malignant phenotype in ovarian cancer.
(Submitter supplied) Side population (SP) cells harbor malignant phenotypes, such as sphere forming capacity, single cell clonogenicity and in vivo tumorigenicity. These malignant phenotypes are related to a poor prognosis for women with ovarian cancer. The aim of this study was to identify key factor(s) that increase the proportion of ovarian cancer SP cells through a functional genomics screen. A library of 81 000 shRNAs targeting 15 000 genes was transfected into CH1 and SKOV3 cells, followed by SP analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117480/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482311
Series		Accession: GSE117480	ID: 200117480

1822. ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101834/
Series		Accession: GSE101834	ID: 200101834

1823. ETS1 induction by the omental microenvironment promotes ovarian cancer metastasis [RNA-Seq]
(Submitter supplied) ETS1 expression is induced by the microenvironment of ovarian metastasis and this expression allows ETS1 to activate a gene expression program involved in cell invasion and epithelial mesenchymal transision.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101833/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395682
Series		Accession: GSE101833	ID: 200101833

1824. MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107073/
Series		Accession: GSE107073	ID: 200107073

1825. MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [inhibitor MRT199665]
(Submitter supplied) In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that transgenic Mef2cS222A/S222A mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418960
Series		Accession: GSE107071	ID: 200107071

1826. MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [mutant MEF2C]
(Submitter supplied) In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using functional proteomics of patient AML specimens, we identified MEF2C S222 phosphorylation as a specific marker of primary chemoresistance. We found that transgenic Mef2cS222A/S222A mice engineered to block MEF2C phosphorylation exhibited normal hematopoiesis, but were resistant to leukemogenesis induced by MLL-AF9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369743
Series		Accession: GSE94453	ID: 200094453

1827. L1CAM dependent transcriptional programs in brain metastatic cells
(Submitter supplied) L1CAM dependent gene expression programs in vitro and ex vivo were analyzed by translating ribosome affinity purification and sequencing (TRAP-Seq).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82281/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324544
Series		Accession: GSE82281	ID: 200082281

1828. EpCAM Based Capture Detects and Recovers Circulating Tumor Cells From  Subtypes of Breast Cancer Except Claudin-low
(Submitter supplied) Circulating tumor cells (CTCs) potential utility as a liquid biopsy is of great interest in breast cancer.  The goal of this study is to use RNA-seq to show that we can capture CTCs  using EpCAM based gating for most of the breast cancer subtypes and detection of breast cancer specific genese are independent of sequencing plateformt. Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the hg 18. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL14761 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71192/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA290550
Series		Accession: GSE71192	ID: 200071192

1829. Histone variant macroH2A1 rewires carbohydrate and lipid metabolism of hepatocellular carcinoma cells towards cancer stem cells
(Submitter supplied) We recently described the phenotype of HepG2 and Huh-7 hepatocellular carcinoma cells deleted for histone variant macroH2A1, which acquire cancer stem cell phenotype (Lo Re O et al., Hepatology 2017, PMID: 28913935). We found that short hairpin RNA-mediated macroH2A1 knockdown induces acquisition of CSC-like features, including the growth of significantly larger and less differentiated tumors when injected into nude mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117459/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA482150
Series		Accession: GSE117459	ID: 200117459

1830. Cigarette smoke and pancreatic cancer: Evidence for increased pancreatic cancer stem cell population
(Submitter supplied) Cigarette smoking is one of the major risk factors for Pancreatic Cancer. Our goal in this study is to investigate mechanistic link between smoking and pancreatic cancer stem cell (CSC) enrichment. We report that cigarette smoking augments pancreatic CSCs and this process occurs by the activation of Paf1/PD2, a major stem ness marker. We also report that the cigarette smoke activates Paf1/PD2 through nACHRα7-ERK1/2-FOSL1 signaling axis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101726/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395302
Series		Accession: GSE101726	ID: 200101726

1831. The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL10558 GPL11154 84 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117182/
Series		Accession: GSE117182	ID: 200117182

1832. The miR-96 and RARG signaling axis governs androgen signaling and prostate cancer progression V
(Submitter supplied) Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARG), are commonly reduced in prostate cancer (PCa). Therefore we sought to establish the cellular and gene regulatory consequences of reduced RARG expression, and determine RARG regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARG levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117110/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481061
Series		Accession: GSE117110	ID: 200117110

1833. Amlexanox targets the IKK-ɛ/TBK1/NF-κB signaling axis to suppress the epithelial-to-mesenchymal transition and prostate cancer metastasis
(Submitter supplied) Tumor metastasis is the major cause of death for prostate cancer (PCa) patients. However, the treatment options for metastatic PCa are very limited. Epithelial-mesenchymal transition (EMT) has been reported to be an indispensable step for tumor metastasis and is suggested to associate with acquisition of cancer stem cell (CSC) attributes. Herein we establish a EMT reporter system based on firefly or renilla luciferase reporter driven by promoters of CDH1 and VIM genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110206/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433172
Series		Accession: GSE110206	ID: 200110206

1834. Cryptic promoter activation drives POU5F1 (OCT4) expression in renal cell carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 26 Samples
FTP download: GEO (BED, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117324/
Series		Accession: GSE117324	ID: 200117324

1835. Genome-wide chromatin accessibility and gene expression profiling of renal cell carcinoma and matched normal kidney tubules [RNA-Seq]
(Submitter supplied) We generated primary cultures from renal cell carcinoma and matched normal primary kidney cortex tubule cell cultures from 3 patients. Early passage cultures of these two cell types were subjected to chromatin accessibility profiling (DNase-seq) and gene expression profiling (RNA-seq). Studying these paired and patient-matched controlled data sets will shed light on the epigenomic changes that underlie transformation of kidney tubules into malignant cancers.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481757
Series		Accession: GSE117313	ID: 200117313

1836. Translational control through differential ribosome pausing during amino acid limitation in mammalian cells
(Submitter supplied) Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of tRNA charging, which regulates translation through ribosome pausing at two of six arginine codons. Interestingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 34 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113751/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453915
Series		Accession: GSE113751	ID: 200113751

1837. RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas
(Submitter supplied) Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-Seq analysis of laser-microdissected melanocytic nevi (n=23) and primary melanoma samples (n=57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 80 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112509/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448014
Series		Accession: GSE112509	ID: 200112509

1838. The influence of PPFIA1 silencing to gene expression in breast carcinoma cell line and head and neck squamous cell carcinoma cell lines by RNA-sequencing in three dimensional collagen I
(Submitter supplied) PPFIA1 (encodes for liprin-α1) locates at the commonly amplified 11q13 region in cancer, but the precise mechanism of liprin-α1 function has remained unclear. In this study we show how genes are differentially expressed after liprin-α1 knockdown in different cell lines, grown in three dimensional matrix. The overall goal was to gain insight into the mechanism by which liprin-α1 has an effect on the progression of head and neck carcinomas and breast carcinomas in three dimensional environment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427125
Series		Accession: GSE108392	ID: 200108392

1839. Inhibition of the Aryl Hydrocarbon Receptor - Polyamine Biosynthesis Axis Suppresses Multiple Myeloma and prostate cancer progression
(Submitter supplied) Polyamine inhibition for cancer therapy is, conceptually, an attractive approach but has yet to meet success in the clinical setting. The aryl hydrocarbon receptor (AHR) is the central transcriptional regulator of xenobiotic response. Our study revealed that AHR also positively regulated intracellular polyamine production via direct transcriptional activation of two genes (ODC1 and AZIN1) involved in polyamine biosynthesis and control, respectively. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117160/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA481382
Series		Accession: GSE117160	ID: 200117160

1840. Towards minimal residual disease-directed therapy in melanoma
(Submitter supplied) Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics, yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD we applied single-cell RNA-sequencing to malignant cells isolated from BRAF-mutant patient-derived xenograft (PDX) melanoma cohorts exposed to concurrent RAF/MEK-inhibition.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL18573 865 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477841
Series		Accession: GSE116237	ID: 200116237

1841. Stem cell functionality is microenvironmentally defined during tumor expansion and therapy response in colon cancer
(Submitter supplied) Solid malignancies have been speculated to depend on cancer stem cells (CSCs) for expansion and relapse after therapy. Here we report on quantitative analyses of lineage tracing data from primary colon cancer xenograft tissue to assess CSC functionality in a human solid malignancy. The temporally obtained clone size distribution data support a model in which stem cell function in established cancers is not intrinsically but entirely spatiotemporally orchestrated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95499/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377285
Series		Accession: GSE95499	ID: 200095499

1842. Overall expression of genes in CRYM overexpressed Prostate cancer cell line LNCaP
(Submitter supplied) RNA sequencing was employed to profile the entire mRNA transcripts. Total RNA from LNCaP transfected with control vector or CRYM bearing vector was isolated. RNA and samples were subjected to the sequencing on illumina's HiSeq 4000 platform. RNA-seq revealed the expression of 58,540 transcripts and of 34,878 (59.6 %) genes were expressed in LNCaP cells. 3226 (9.25 %) genes were altered by CRYM and 2.72 % were upregulated and 6.53 % were downregulated.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101525/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394730
Series		Accession: GSE101525	ID: 200101525

1843. Multi-omics analysis of mutant and wild-type β-catenin networks
(Submitter supplied) This study describes the systematic transcriptomic and expression and interaction proteomic analysis of isogenic HCT116 colorectal cancer cells with either mutant CTNNB1/Beta-catenin allele disrupted or wild-type CTNNB1/Beta-catenin allele disrupted.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95670/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377883
Series		Accession: GSE95670	ID: 200095670

1844. miR-205 mediates adaptive resistance to MET inhibition via ERRFI1 targeting and raised EGFR signaling
(Submitter supplied) The onset of secondary resistance represents a major limitation to long term efficacy of target therapies in cancer patients. Thus, the identification of mechanisms mediating secondary resistance is key to the rational design of alternative therapeutic strategies for resistant patients. MiRNA profiling combined with RNA-seq in MET-addicted gastric and lung cancer cell lines led us to identify the miR-205/ERRFI1 (ERBB receptor feedback inhibitor-1) axis as a novel mediator of resistance to MET tyrosine kinase inhibitors (TKIs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114406/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451125
Series		Accession: GSE114406	ID: 200114406

1845. The homeobox transcription factor HB9 induces senescence and blocks differentiation in hematopoietic stem and progenitor cells
(Submitter supplied) The translocation t(7;12)(q36;p13) occurs in infants and very young children with AML and usually has a fatal prognosis. Whereas the transcription factor ETV6, located at chromosome 12p13, has largely been studied in different leukemia types, the influence of the translocation partner HB9 (chr. 7q36), is still unknown. This is particularly surprising as ectopic expression of HB9 is the only recurrent molecular hallmark of translocation t(7;12) AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117060/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480958
Series		Accession: GSE117060	ID: 200117060

1846. CD73 knockdown effect in pancreatic cancer cell lines
(Submitter supplied) Recent studies have shown that non-enzymatic function of CD73 play a key role in tumor progression, but this function of CD73 in pancreatic cancer cells has not been studied. In the present study, PANC-1 cell lines were transfected with CD73 siRNA, and proliferation ability and cell cycle was significantly inhibited. However, little is known about the mechanisms involved in CD73 regulation in tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE117nnn/GSE117012/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480855
Series		Accession: GSE117012	ID: 200117012

1847. A novel enhancer regulates MGMT expression and promotes temozolomide resistance in glioblastoma
(Submitter supplied) Temozolomide (TMZ) has been used for the treatment of glioblastoma (GBM) since last decade, but its treatment benefits are limited by acquired resistance, a process that remains incompletely understood. Here we report that a novel enhancer, located between the promoters of Ki67 and O6-methylguanine-DNA-methyltransferase (MGMT) genes, is activated in TMZ-resistant patient-derived xenograft (PDX) lines as well as in recurrent tumor samples. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113816/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454033
Series		Accession: GSE113816	ID: 200113816

1848. Ribosome profiling and transcriptome profiling of MCF-7 cells
(Submitter supplied) We performed ribosome profiling (RIBO-seq) and transcriptome profiling (RNA-seq) to monitor RNAs associated with ribosome in the MCF-7 cell model Keywords: ribosome profiling, translation, MCF-7
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438445
Series		Accession: GSE111866	ID: 200111866

1849. Transcriptional properties of estrogen receptor fusion genes.
(Submitter supplied) RNA sequencing (RNA-seq) detects estrogen receptor alpha gene (ESR1) fusion transcripts in estrogen receptor positive (ER+) breast cancer but their role in disease pathogenesis remains unclear.  Herein we examined multiple in-frame and out-of-frame ESR1 fusions and found that two, both identified in advanced endocrine treatment resistant disease, encoded stable and functional in-frame fusion proteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116170/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477539
Series		Accession: GSE116170	ID: 200116170

1850. XPO1 inhibition antagonizes MCL via nuclear retention of IkB: Selinexor demonstrates antitumor activities in both ibr-sensitive and ibr-resistant tumor cells
(Submitter supplied) Inhibition of BCR signaling through BTK inhibitor, ibrutinib, has generated a remarkable response in mantle cell lymphoma (MCL).  However, approximately one-third of the patients do not respond well to the drug and disease relapse on ibrutinib is nearly universal.  Alternative therapeutic strategies aimed to prevent and overcome ibrutinib resistance are needed.  We compared and contrasted the effects of selinexor, a selective inhibitor of nuclear export, with ibrutinib in six MCL cell lines that display differential intrinsic sensitivity to ibrutinib. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480275
Series		Accession: GSE116810	ID: 200116810

1851. A robust qualitative transcriptional signature for the early diagnosis of gastric cancer
(Submitter supplied) Pathological examination of gastroscopy biopsy specimens will make false diagnosis for gastric cancer (GC) due to inaccurate sampling locations and/or insufficient sampling amount. We extracted a robust qualitative transcriptional signature, based on the within-sample relative expression orderings (REOs) of gene pairs, to discriminate both GC tissues and adjacent-normal tissues from non-GC gastritis and normal gastric tissues.The qualitative transcriptional signature can be robustly applied at the individual level to aid the diagnosis of early GC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116782/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480243
Series		Accession: GSE116782	ID: 200116782

1852. Genome-wide identification of protein binding sites in mammalian cells.
(Submitter supplied) We report the application of genome-wide protein binding sites capture (GWPBS-Cap) technology for high-throughput profiling of protein binding sites in mammalian cells. By obtaining over 37 billion bases of sequence from NaCl washed chromatin DNA in each group, we got an unprecedented view into genome-wide binding patterns of many DNA binding proteins of Hela cells. We find that active promoters contain more PBSs with lower NaCl tolerance and our technology provides a genome-wide landscape of DNA-protein interactions.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL23227 GPL20301 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA480206
Series		Accession: GSE116770	ID: 200116770

1853. P68-associated lncRNA LOC284454 is differentially expressed in human cancers and modulates gene expression
(Submitter supplied) DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 75 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393630
Series		Accession: GSE101050	ID: 200101050

1854. Effect of hyperfractionated irradiation (HFRT) of prostate primary basal cells (PrEPs) on the transcriptome
(Submitter supplied) We irradiated PrEPs derived from four patients undergoing radical prostatectomy according to a HFRT protocol (20 single treatments). Transcriptome was analysed by NextGen sequencing. Gene expression profiling revealed a dysregulation of 3468 genes at mRNA level (1470 upregulated and 1998 downregulated). We could characterize cells surviving the lethal effects of radiation by two gene expression signatures showing that these cells have low expression of genes related to DNA damage response and Interferon signaling pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112686/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448743
Series		Accession: GSE112686	ID: 200112686

1855. SALL4 Crud ChIP sequencing-WT and RNA-seq of SNU398 cells treated with therapeutic SALL4 peptides
(Submitter supplied) SALL4 is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in HCC, a malignancy with no effective treatment. In cancer cells, SALL4 associates with NuRD to silence tumor suppressor genes such as PTEN. Here, we design a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4-NURD interaction using systematic truncation and amino acid substitution studies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL22790 7 Samples
FTP download: GEO (BW, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA448843
Series		Accession: GSE112729	ID: 200112729

1856. Anti-Tumor Activity of Entrectinib, a Pan-TRK, ROS1 and ALK Inhibitor, in ETV6-NTRK3-Positive Acute Myeloid Leukemia
(Submitter supplied) Activation of TRK family tyrosine kinases by chromosomal rearrangement has been shown to drive a wide range of solid tumors and hematologic malignancies. TRK fusions are actionable targets as evidenced by recent clinical trial results in solid tumors. Entrectinib (RXDX-101) is an investigational, orally available, CNS-active, highly potent and selective kinase inhibitor with low nanomolar potency against TRKA/B/C, ROS1 and ALK kinase activities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100885/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393349
Series		Accession: GSE100885	ID: 200100885

1857. Iron-mediated stabilization of PCBP1 post-transcriptionally promotes GM-CSF production during autoimmune pathogenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21273 GPL13112 GPL11154 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84702/
Series		Accession: GSE84702	ID: 200084702

1858. Transcriptome targets of PCBP1 in T cells identified with CLIP
(Submitter supplied) Iron deposition is frequently observed in human autoinflammatory diseases, such as in the brain of patients with multiple sclerosis or in the synovial fluid of patients with rheumatoid arthritis1-5.  Yet, the functional outcome of excessive iron in inflammatory conditions is largely unknown. Granulocyte macrophage colony-stimulating factor (GM-CSF) is a proinflammatory cytokine promoting myeloid cell maturation and activation6 and is essential for the pathogenesis of many autoimmune diseases, including autoimmune encephalomyelitis7-10. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84700/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330855
Series		Accession: GSE84700	ID: 200084700

1859. mRNA profiles of JMJD3 overexpression NB4 cells
(Submitter supplied) Next Generation Sequencing Facilitates Quantitative Analysis of NB4 cells transduced with control or JMJD3-expression vector.  JMJD3, a stress-inducible H3K27 demethylase, plays a critical regulatory role in the initiation and progression of malignant hematopoiesis. However, how this histone modifier effects in a cell type-dependent manner remains unclear. Here, we show that in contrast to its oncogenic effect in preleukemia state and lymphoid malignancies, JMJD3 relieves the differentiation-arrest of certain subtypes (such as M2 and M3) of acute myeloid leukemia (AML) cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116499/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478849
Series		Accession: GSE116499	ID: 200116499

1860. KDM5 histone demethylases repress innate immune response via suppression of STING
(Submitter supplied) Tri-methylation on histone H3 lysine 4 (H3K4me3) is enriched near transcription start sites and correlates with active transcription. Like other histone marks, methylation on H3K4 is catalyzed by the respective methyltransferases and erased by demethylases. Lysine demethylase 5 (KDM5) family of Fe (II) and α-ketoglutarate-dependent dioxygenases removes the methyl groups from H3K4me3. All four family members of KDM5 demethylases (KDM5A-D) share sequence identity, have similar in vitro kinetic parameters, and display functional redundancy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108502/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427473
Series		Accession: GSE108502	ID: 200108502

1861. Gene dosage effect of CUX1 in a murine model disrupts HSC homeostasis and controls the severity and mortality of MDS.
(Submitter supplied) Monosomy 7 (-7) and del(7q) are high-risk cytogenetic abnormalities common in myeloid malignancies. We previously reported that CUX1, a homeodomain-containing transcription factor encoded on 7q22, is frequently inactivated in myeloid neoplasms, and CUX1 myeloid tumor suppressor activity is conserved from humans to Drosophila. CUX1-inactivating mutations are recurrent in clonal hematopoiesis of indeterminate potential as well as myeloid malignancies, in which they independently carry a poor prognosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101300/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393970
Series		Accession: GSE101300	ID: 200101300

1862. Single-molecule nascent RNA sequencing reveals regulatory domain architecture ant promoters and enhancers
(Submitter supplied) CoPRO adapts PRO-cap for paired end sequencing, and includes a total of three different libraries that were enriched for either capped nascent RNAs only, uncapped nascent RNAs only, or both.  With paired end sequencing, each read tells us where an RNA polymerase molecule initiated, and then where its active site is located.  Comparison of the libraries for different capping states allows us identify the precise location of pausing, and of where nascent RNAs become capped across the tens of thousands of initiation sites that we detect. more...
Organism:	Homo sapiens; Mus musculus
Type:		Other; Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 14 Samples
FTP download: GEO (BW, RDATA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116472/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478717
Series		Accession: GSE116472	ID: 200116472

1863. Single-Cell Transcriptome Analysis of Lineage Diversity and Microenvironment in High-Grade Glioma
(Submitter supplied) Despite extensive molecular characterization, we lack a comprehensive picture of lineage identity, differentiation, and microenvironmental composition in high-grade gliomas (HGGs). We sampled the cellular milieu of HGGs with massively-parallel single-cell RNA-Seq. While HGG cells can resemble glia or even immature neurons and form branched lineage structures, mesenchymal transformation results in unstructured populations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103224/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400576
Series		Accession: GSE103224	ID: 200103224

1864. ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113499/
Series		Accession: GSE113499	ID: 200113499

1865. ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs [RNA-seq]
(Submitter supplied) Aberrant overexpression of oncogenic ETS factors through chromosomal rearrangments is the most common genomic event in primary prostate tumor and these factors have been well studied. Loss of ELF1, another ETS transcription factor family member, is a common event in prostate cancer, but the function of ELF1 has not been described within the prostate. Studies of ELF1 in different tissue types has determined that it can be important for oncogeneis or tumor suppression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (DIFF, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451362
Series		Accession: GSE113485	ID: 200113485

1866. Generation of esophageal organoids from human pluripotent stem cells and their use to study human development
(Submitter supplied) Tracheoesophageal disorders and diseases are prevalent in humans such that an organoid model of human esophagus could be greatly beneficial. We therefore established a three-dimensional esophageal organoid culture system through the directed differentiation of human pluripotent stem cells (hPSCs). We identified that sequential manipulation of several signaling pathways resulted in patterning of definitive endoderm to dorsal anterior foregut spheroids (dAFGs). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112886/
Series		Accession: GSE112886	ID: 200112886

1867. Synergy from Gene Expression and Network Mining (SynGeNet) method predicts genotype-specific synergistic drug combinations in melanoma
(Submitter supplied) Using our computational method SynGeNet to evaluate genomic and transcriptomic data characterizing four major genomic subtypes of melanoma, we selected the top ranked drug combination for BRAF-mutation melanoma for subsequent validaiton. Here we present drug-induced gene expression data from the BRAF-mutant A375 melanoma cell line in response to four treatment conditions: vehicle control (DMSO), vemurafenib alone, tretinoin (ATRA) alone and vemurafenib+tretinoin combination.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109731/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431809
Series		Accession: GSE109731	ID: 200109731

1868. SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL20301 GPL18573 337 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108397/
Series		Accession: GSE108397	ID: 200108397

1869. SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [10x]
(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from 10x Genomics platform was analyzed to dissect this problem at multiple scales. Data indicates that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108394/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427130
Series		Accession: GSE108394	ID: 200108394

1870. SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [Fluidiam scRNA-Seq]
(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the SMART-seq/Fluidigm and 10x Genomics platforms were analyzed to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 327 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427110
Series		Accession: GSE108383	ID: 200108383

1871. SAKE (Single-cell RNA-Seq Analysis and Klustering Evaluation) Identifies Markers of Resistance to Targeted BRAF Inhibitors in Melanoma Cell Populations [Bulk RNA-Seq]
(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the SMART-seq/Fluidigm and 10x Genomics platforms were analyzed to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108382/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427111
Series		Accession: GSE108382	ID: 200108382

1872. RNA sequencing of 13 T-cell acute lymphoblastic leukemia patients (5 TCRAD-MYC translocated T-ALL_8TAL1-LMO2 T-ALL)
(Submitter supplied) RNA sequencing analysis revealed a different expression profile between two different T-ALL subgroups, namely MYC-TCRAD translocated T-ALL vs TAL1-LMO2 T-ALL.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 13 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106699/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417699
Series		Accession: GSE106699	ID: 200106699

1873. LncRNA NMR knockdown and overexpression in esophageal squamous cell carcinoma cell lines
(Submitter supplied) Long noncoding RNAs (lncRNAs) are emerging as key regulators in cancer and play complicate and critical roles in regulating various key biological processes including chromatin modification, transcription and post-transcriptional processing. We identified a novel transcript, lncRNA NMR, which was upregulated in esophageal squamous cell carcinoma (ESCC) and significantly associated with overall survival of ESCC patients and and is identical to ENST00000432429.1 in GENCODE v13 or ENST00000432429.5 in Ensembl release 83. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101743/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395325
Series		Accession: GSE101743	ID: 200101743

1874. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition and tumorigenesis of non-small cell lung cancer
(Submitter supplied) Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues, and by providing binding platforms for “reader” proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Recently, we identified the YEATS domain of AF9 as a novel acetyllysine-binding module, and showed that the ENL YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BW, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100347/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391417
Series		Accession: GSE100347	ID: 200100347

1875. Global transcriptome analysis of BJAB cells that are modulated by EBV infection or (and) EBV BART6-3p mimics.
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of EBV infection or (and) EBV BART6-3p mimics on the global transcriptome of the BJAB cells. Methods: BJAB cells were transfected with negative control mimics or BART6-3p mimics for 48 h and then infected with EBV virons for 2h. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95634/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377734
Series		Accession: GSE95634	ID: 200095634

1876. Hepatic transcriptome of pediatric hepatoblastoma.
(Submitter supplied) The mechanisms underlying hepatoblastoma are not well defined.  To address this, we generated transcriptomic profiles of normal, background, and hepatoblastoma liver samples from patients aged 0.01 months to 6 years, using RNA-sequencing.  Hepatoblasoma was histologically confirmed.  Here we focus on the elevation of stem cell markers and the loss of tumor suppressor proteins leading to the development of hepatoblastoma in very young children.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 32 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323460
Series		Accession: GSE81928	ID: 200081928

1877. Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL9115 20 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79778/
Series		Accession: GSE79778	ID: 200079778

1878. Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation [RNA-Seq]
(Submitter supplied) HER2 is a transmembrane receptor tyrosine kinase, which plays a key role in breast cancer due to a common genomic amplification. It is used as a marker to stratify patients in the clinic and is targeted by a number of drugs including Trastuzumab and Lapatinib. HER2 has previously been shown to translocate to the nucleus. In this study, we have explored the properties of nuclear HER2 by analysing the binding of this protein to the chromatin in three breast cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 10 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79776/
Series		Accession: GSE79776	ID: 200079776

1879. A widespread alternate form of cap-dependent mRNA translation initiation
(Submitter supplied) We report the application of polysome profiling sequencing technology for high-throughput transcriptomics and translatomics in mammalian cells. We compare reduction of Dap5 to control in metastatic breast cancer cells in transcription and polysome enriched translation using RNA sequencing. Genome-wide transcriptomic and translatomic analyses indicate that DAP5 is required for translation of many transcription factor and receptor capped mRNAs and their mRNA targets involved in cell survival, motility, DNA repair and translation initiation, among other mRNAs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115142/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473917
Series		Accession: GSE115142	ID: 200115142

1880. tRNA-derived small non-coding RNAs (tDRs) as novel predictive biomarkers for trastuzumab-resistant breast cancer.
(Submitter supplied) Background: Resistance to trastuzumab remains a common challenge to HER-2 positive breast cancer. Up until now, the underlying mechanism of trastuzumab resistance is still unclear. tRNA-derived small non-coding RNAs (tDRs), a new class of small non-coding RNA (sncRNAs), have been observed to play an important role in cancer progression. However, the relationship between tDRs and trastuzumab resistance is still unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107473/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420202
Series		Accession: GSE107473	ID: 200107473

1881. Chromatin landscape of human visceral and subcutaneous adipocytes
(Submitter supplied) Obesity is characterized by the excess of body fat leading to impaired health. Abdominal fat is particularly harmful and is associated with cardiovascular and metabolic diseases and cancer. In contrast, subcutaneous fat is generally considered less detrimental. The mechanisms that establish the cellular characteristics of these distinct fat types in humans are not fully understood. Here, we explored whether differences of their gene regulatory mechanisms can be investigated in vitro. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL20301 22 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102638/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398252
Series		Accession: GSE102638	ID: 200102638

1882. KMT2C medaites the estrogen dependence of breast cancer through regulation of ERα enhancer function
(Submitter supplied) KMT2C is a key regulator of ERα activity whose loss allows for hormone independent proliferation in MCF7 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 47 Samples
FTP download: GEO (BIGWIG, BW, PNG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100328/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391343
Series		Accession: GSE100328	ID: 200100328

1883. RNA-Seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature
(Submitter supplied) Improving outcomes in multiple myeloma will not only involve development of new therapies, but better use of existing treatments. We performed RNA sequencing (RNA-Seq) on samples from newly diagnosed patients enrolled into the phase II PADIMAC study. Using an empirical Bayes approach and synthetic annealing, we developed and trained a seven-gene signature to predict treatment outcome. We tested the signature on independent cohorts treated with bortezomib- and lenalidomide-based therapies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 44 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116324/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478148
Series		Accession: GSE116324	ID: 200116324

1884. A role for p53 in the adaptation to glutamine starvation through the expression of Slc1a3
(Submitter supplied) Numerous mechanisms to support cells under conditions of transient nutrient starvation have been described. The tumor suppressor protein p53 can contribute to the adaptation of cells to metabolic stress through various mechanisms that may help cancer cell survival in nutrient limiting conditions. We show here that p53 helps cancer cells to survive glutamine starvation by promoting the expression of SLC1A3, an aspartate/glutamate transporter that allows the utilization of aspartate to support cells in the absence of extracellular glutamine. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116087/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476993
Series		Accession: GSE116087	ID: 200116087

1885. Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL16791 GPL18573 66 Samples
FTP download: GEO (CSV, MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114727/
Series		Accession: GSE114727	ID: 200114727

1886. Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing
(Submitter supplied) Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 56 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114725/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472383
Series		Accession: GSE114725	ID: 200114725

1887. Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing
(Submitter supplied) Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 10 Samples
FTP download: GEO (CSV, MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114724/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472381
Series		Accession: GSE114724	ID: 200114724

1888. Decreased TGFBR3/Betaglycan expression enhances the metastatic abilities of renal cell carcinoma cells through TGF-b-dependent and independent mechanisms
(Submitter supplied) It is unclear how the loss of TGF-b signaling components affects metastatic abilities in clear cell renal cell carcinoma (ccRCC). In this study, we identified that low TGFBR3 expression in ccRCC cells enhanced primary tumor formation and lung metastasis. In the presence of TGFBR3, TGF-b2 decreased the aldehyde dehydrogenase (ALDH)-positive ccRCC cell population, in which renal cancer-initiating cells are enriched. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106719/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417759
Series		Accession: GSE106719	ID: 200106719

1889. Screening microRNA-196 targets in 11q23-translocation acute myeloid leukemia reveal mechanisms maintaining leukemia stemness with therapeutic potential
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL6244 26 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75843/
Series		Accession: GSE75843	ID: 200075843

1890. Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13
(Submitter supplied) High-grade serous ovarian cancer is characterized by extensive copy number alterations, among which the amplification of MYC oncogene occurs in nearly half of tumors. We demonstrate that ovarian cancer cells highly depend on MYC for maintaining their oncogenic growth, indicating MYC as a therapeutic target for this difficult-to-treat malignancy.  However, targeting MYC directly has proven difficult. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE116nnn/GSE116282/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA478056
Series		Accession: GSE116282	ID: 200116282

1891. Next Generation Sequencing Facilitates Quantitative Analysis of human patient derived primary Glioblastoma (GBM) cancer cell Transcriptomes
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare GBM transcriptome profiling (RNA-seq) after shRNA based knockdown of PRKAB1 and to compare gene expression by optimal high-throughput data analysis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324266
Series		Accession: GSE82183	ID: 200082183

1892. RNA-seq of cells with TET1 knockout
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115580/
Series		Accession: GSE115580	ID: 200115580

1893. RNA-seq of Hs578T cells with TET1 knockout
(Submitter supplied) Both gains and losses of DNA methylation are common in cancer but the factors controlling this methylation balance remain unclear. Triple negative breast cancer (TNBC), a subtype that does not overexpress hormone receptors or HER2/NEU is one of the most hypomethylated cancers observed. In search for an explanation for this, we discovered that the TET1 DNA demethylase is specifically overexpressed in about 40% of patients with TNBC, where it is associated with hypomethylation of up to 10% of queried CpG sites and a worse overall survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475534
Series		Accession: GSE115578	ID: 200115578

1894. HNF4alpha P1 and P2 isoforms regulate different gene networks in the colorectal cancer cell line Caco2/15.
(Submitter supplied) The nuclear receptor HNF4alpha is a master regulator of gene transcription in intestinal epithelial cells where P1 and P2 isoforms are expressed. HNF4alpha has been associated with colorectal cancer  where its role remains controverisal since both tumor suppressor and  oncogene characteristics have been observed. Evidences gathered from mouse models suggested however that this controversy on HNF4alpha function in colorectal cancer could be explained by the different functions of its two isoforms classes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106378/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416506
Series		Accession: GSE106378	ID: 200106378

1895. Cooperation between TLX1 and the NUP214-ABL1/STAT5 signaling in T-cell acute lymphoblastic leukemia
(Submitter supplied) The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associated with overexpression of the TLX1 or TLX3 transcription factors in T-cell acute lymphoblastic (T-ALL). Here we show that NUP214-ABL1 kinase cooperates with TLX1 in driving T-ALL development using a transgenic mouse model. Using ChIP-seq and ATAC-seq, we show that TLX1 and STAT5, the downstream effector of NUP214-ABL1, selectively increase the accessibility of enhancer regions, and cooperatively activate the expression of key proto-oncogenes such as MYC and BCL2. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 69 Samples
FTP download: GEO (BEDGRAPH, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397010
Series		Accession: GSE102209	ID: 200102209

1896. Microfluidics-based molecular profiling of circulating tumor cells in checkpoint inhibitor immunotherapy and BRAF/MEK-treated melanoma patients
(Submitter supplied) Gene expression profiling of circulating tumor cells-enriched cells obtained from blood of three melanoma patients on immunotherapy.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100565/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392120
Series		Accession: GSE100565	ID: 200100565

1897. RNA-seq of MDA-MB-231 cells with TET1 knockout
(Submitter supplied) DNA hypermethylation is known to contribute to the formation of cancer.  However, DNA hypomethylation has received far less attention and the factors controlling the balance between hypo and hypermethylation and its impact on tumorigenesis remains unclear.  Triple negative breast cancer (TNBC), a subtype of breast cancer that does not overexpress the hormone receptors or HER2/NEU, is one of the most hypomethylated cancers observed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100483/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391938
Series		Accession: GSE100483	ID: 200100483

1898. Sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies
(Submitter supplied) The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Non-specific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published datasets. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other
Platform: GPL16791 26 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85163/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336359
Series		Accession: GSE85163	ID: 200085163

1899. Widespread intronic polyadenylation inactivates tumor suppressor genes in leukemia
(Submitter supplied) DNA mutations are known cancer drivers.  Here, we investigated if mRNA events that are upregulated in cancer can functionally mimic the outcome of genetic alterations.  3′-seq or RNA-seq were applied to normal and malignant B cells from chronic lymphocytic leukemia (CLL; N = 59).  We discovered widespread upregulation of truncated mRNAs and proteins in primary CLL cells that were not generated by genetic alterations but occurred through intronic polyadenylation (IPA). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111793/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438149
Series		Accession: GSE111793	ID: 200111793

1900. T cell landscape of non-small cell lung cancer revealed by deep single-cell RNA sequencing
(Submitter supplied) Cancer immunotherapies have shown sustained clinical responses in treating non-small cell lung cancer (NSCLC), but the clinical outcome is not uniform among patients, with complex tumour-immune interactions playing key roles. To depict and dissect the baseline landscape of the composition, lineage and functional states of tumor-infiltrating lymphocytes (TILs) in lung cancer, here we generated deep single-cell RNA sequencing data for 12346 T cells from the tumour, adjacent normal tissues and peripheral blood from 14 treatment-naïve NSCLC patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99254/
Series		Accession: GSE99254	ID: 200099254

1901. Differential gene expression of tissue-resident memory and effector memory T cells in breast cancer
(Submitter supplied) Two infiltrating T cell populations (CD8+CD69+CD103+ and CD8+CD69+CD103-) were isolated from 3 breast cancer tumors by FACS for gene expression profiliing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110938/
Series		Accession: GSE110938	ID: 200110938

1902. Single-cell RNA-seq of six thousand purified CD3+ T cells from human primary TNBCs
(Submitter supplied) CD3+ T cells were isolated by FACS from primary tumour tissues of two triple-negative breast cancer patients. Sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation were done according to the protocol supplied by the manufacturer. Libraries were sequenced on an Illumina HiSeq 2500 High Output Mode using V4 clustering and sequencing chemistry to achieve 100 bp paired-end reads.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110686/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434278
Series		Accession: GSE110686	ID: 200110686

1903. Transcriptomic sequencing after MALAT1 knockdown in A431 cells
(Submitter supplied) Cutaneous squamous cell carcinoma (CSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. In this study, metastasis-associated in lung adenocarcinoma transcript 1 (MALAT1), a long non-coding RNA, was identified to be significantly up-regulated in CSCC tumors and cell lines. We conducted RNA sequencing to characterize gene expression changes in MALAT1-silenced cutaneous squamous cell carcinoma cells (A431).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100399/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391569
Series		Accession: GSE100399	ID: 200100399

1904. POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 88 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115124/
Series		Accession: GSE115124	ID: 200115124

1905. POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer [RNA-seq]
(Submitter supplied) Transcriptome analysis by high throughput sequencing
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115122/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473832
Series		Accession: GSE115122	ID: 200115122

1906. Neuroendocrine prostate cancer models
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112830/
Series		Accession: GSE112830	ID: 200112830

1907. Molecular characterization of neuroendocrine prostate cancer organoids and PDOX by RNA-seq
(Submitter supplied) We report the generation and characterization of tumor organoids and PDOX derived from needle biopsies of metastatic lesions from neuroendocrine prostate cancer patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112786/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449096
Series		Accession: GSE112786	ID: 200112786

1908. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade
(Submitter supplied) Chromatin regulators play a broad role in regulating gene expression, and when gone awry, can lead to cancer. Here we demonstrate that ablation of the histone demethylase LSD1 in cancer cells increases repetitive element expression, including ERVs, and decreases expression of RNA-induced silencing complex (RISC) components. Significantly, this leads to dsRNA stress and activation of type 1 interferon, which stimulates anti-tumor T cell immunity and restrains tumor growth. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL19057 GPL16791 29 Samples
FTP download: GEO (BW, CSV, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445303
Series		Accession: GSE112230	ID: 200112230

1909. Regulation of alternative splicing induced by paclitaxel in human non-small cell lung cancer
(Submitter supplied) RNA-seq was performed on A549 cells treated with paclitaxel or control, in order to profile the alternative splicing events that were regulated upon paclitaxel treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107676/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421002
Series		Accession: GSE107676	ID: 200107676

1910. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space
(Submitter supplied) Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we present genome-scale maps of DNA methylation in matched primary and recurring glioblastoma tumors, using data from a highly annotated clinical cohort that was selected through a national patient registry. We demonstrate the feasibility of DNA methylation mapping in a large set of routinely collected FFPE samples, and we validate bisulfite sequencing as a multipurpose assay that allowed us to infer a range of different genetic, epigenetic, and transcriptional characteristics of the profiled tumor samples. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL21290 GPL20301 GPL11154 579 Samples
FTP download: GEO (BED, RPKM, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100351/
Series		Accession: GSE100351	ID: 200100351

1911. Transcriptome-wide analysis to determine miR-200a targets in melanoma cell lines
(Submitter supplied) Three metastatic melanoma cell lines (BD-0548-ME, DP-0574-ME and WP-0614-ME) were transfected with miR precursors; we used hsa-miR negative control (NC) or hsa-miR-200a-3p precursors (miR-200a). The objective of this experiment was to determine miR-200a tagerts in melanoma cell lines. We selected low -miR-200a expression cells and then we overexpresed miR-200a or NC. Finally, we compared metastatic melanoma cells overexpressing miR-200a (miR-200a) to the same cell line but overexpressing negative control miR (NC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83512/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326229
Series		Accession: GSE83512	ID: 200083512

1912. BET bromodomain dependency in EWS/ETS driven Ewing Sarcoma
(Submitter supplied) The pathognomonic EWS/ETS fusion transcription factors drive Ewing sarcoma (EWS) by orchestrating an oncogenic transcription program. Therapeutic targeting of EWS/ETS has not been successful; therefore identifying mediators of the EWS/ETS function could offer new therapeutic targets. Here we describe the dependency of chromatin reader BET bromodomain proteins in EWS/ETS driven transcription and investigate the potential of BET inhibitors in treating this lethal cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 22 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113604/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453371
Series		Accession: GSE113604	ID: 200113604

1913. Pancreatic cancer-derived exosomes induce apoptosis of T lymphocytes through the p38 MAPK signal transduction pathway
(Submitter supplied) Pancreatic cancer is the fourth most lethal malignancy, which is characterized by poor immunogenicity. Pancreatic cancer cells take various strategies to suppress host immune response, evade immune defenses, and facilitate tumor growth and development. As a mode of long-range intercellular communication, cancer-derived exosomes contribute to the impairment of the immune system. However, the mechanisms that induce changes in the activities of signal transduction pathways in immune cells, which are influenced by tumor-derived exosomes, are poorly understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476232
Series		Accession: GSE115831	ID: 200115831

1914. JDP2 - an Oncogenic bZIP Transcription Factor in T-cell Acute Lymphoblastic Leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115466/
Series		Accession: GSE115466	ID: 200115466

1915. JDP2 - an Oncogenic bZIP Transcription Factor in T-cell Acute Lymphoblastic Leukemia [RNA-Seq]
(Submitter supplied) A substantial subset of patients with T-cell acute lymphoblastic leukemia (T-ALL) develops resistance to steroids and succumb to their disease. JDP2 encodes a bZIP protein that has been implicated as a T-ALL oncogene from insertional mutagenesis studies in mice, but its role in human T-ALL pathogenesis has remained obscure. Here we show JDP2 is aberrantly expressed in a subset of T-ALL patients and is associated with poor survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475112
Series		Accession: GSE115464	ID: 200115464

1916. Transcriptome-wide analysis of RNA binding and splicing alterations induced by SRSF2 P95 mutations in myelodysplasia
(Submitter supplied) Mutations in the splicing factor Serine Arginine Rich Splicing Factor 2 (SRSF2) occur in over 30% of patients with myelodysplasia (MDS) and a subset of patients with acute myeloid leukemia (AML) and portend a poor prognosis. SRSF2 is ubiquitously expressed and directs exon inclusion or exclusion in a sequence and context dependent manner. SRSF2 mutations almost exclusively affect the proline at position 95 in the C-terminus of the RNA binding domain. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL20301 GPL10999 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111900/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438502
Series		Accession: GSE111900	ID: 200111900

1917. Mutations in the SWI/SNF chromatin remodeling complex induce metabolic rewiring and dependence on oxidative phosphorylation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL23159 GPL13112 24 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109011/
Series		Accession: GSE109011	ID: 200109011

1918. Integrative single-cell analysis reveals human germinal center dynamics de-synchronized in B cell lymphoma
(Submitter supplied) Most adult B cell  lymphomas originate from germinal center (GC) B cells but it is unclear to what extent overt lymphoma B cells retain GC B cell functional dynamics or are blocked in a particular stage of the GC reaction. Here, we used integrative single-cell analysis of phenotype, gene expression and IGH sequence to track the characteristic human GC B cell program in follicular lymphoma (FL) B cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA476067
Series		Accession: GSE115795	ID: 200115795

1919. Expression of TGFβ-inducible myosin-X predicts survival and chemotherapy resistance in squamous cell lung cancer
(Submitter supplied) Squamous cell lung carcinoma (SCC) corresponds to about 25% of all lung cancers. Therapeutic approaches are very limited and platinum-based chemotherapy remains the main treatment option. Despite multiple studies, there are no generally accepted predictive biomarkers for SCC. Transforming growth factor-β (TGFβ) signaling was shown to be implicated in numerous pro-tumorigenic processes, including immune evasion, inflammation and cancer metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377341
Series		Accession: GSE95536	ID: 200095536

1920. Tamoxifen-induced apoptosis of MCF-7 cells via GPR30/PI3K/MAPKs interactions: Verification by ODE modeling and RNA sequencing
(Submitter supplied) Tamoxifen (Nolvadex) is one of the most widely used and effective therapeutic agent for breast cancer. It benefits nearly 75% of patients with ER-positive breast cancer that receive this drug. Its effectiveness is mainly attributed to its capacity to function as an estrogen receptor (ER) antagonist, blocking estrogen binding sites on the receptor, and inhibiting the proliferative action of the receptor-hormone complex. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115737/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475893
Series		Accession: GSE115737	ID: 200115737

1921. SOX9 has distinct regulatory roles in alternative splicing and transcription
(Submitter supplied) SOX9 is known as a crucial transcription factor for various developmental processes and for tissue homeostasis. We examined here its potential role in alternative splicing by analyzing global splicing changes, using RNA-seq of colon tumor cells. We show that SOX9 knockdown alters the splicing of hundreds of genes without affecting their expression levels, revealing that SOX9 controls distinct splicing and transcriptional programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 13 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104103/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA408241
Series		Accession: GSE104103	ID: 200104103

1922. Histone deacetylase inhibitors in alveolar rhabdomyosarcoma
(Submitter supplied) Multiple histone deacetylase inhibitors were tested on multiple alveolar rhabdomyosarcoma cell lines and multiple patient-derived xenograft models of alveolar rhabdomyosarcoma
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115698/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475783
Series		Accession: GSE115698	ID: 200115698

1923. EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association
(Submitter supplied) The transcriptional regulator EVI1 has an essential role in early hematopoiesis and development. However, aberrantly high expression of EVI1 has potent oncogenic properties and confers poor prognosis and chemo-resistance in leukemia and solid tumors. To investigate to what extent EVI1 function might be regulated by posttranslational modifications, we carried out mass spectrometry- and antibody-based analyses and uncovered an ATM-mediated double phosphorylation of EVI1 at the carboxy-terminal S858/S860 SQS motif. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 24 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115643/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475639
Series		Accession: GSE115643	ID: 200115643

1924. Discovery of Selective Estrogen Receptor Covalent Antagonists (SERCAs) for the treatment of ERa(WT) and ERa(MUT) breast cancer.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL20301 GPL570 GPL18573 85 Samples
FTP download: GEO (BED, BW, CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115611/
Series		Accession: GSE115611	ID: 200115611

1925. ML29755 RNA-seq data
(Submitter supplied) Programmed death-ligand 1 (PD-L1) expression has been associated with response to PD-1/PD-L1 inhibition, but responses are also seen in patients with PD-L1 negative tumors when assessed immunohistochemically (IHC) with various antibodies. To help elucidate these findings, we performed a positron emission tomography (PET) imaging study in human with the anti-PD-L1 antibody atezolizumab labeled with Zirconium-89 (89Zr) prior to treatment with atezolizumab to assess normal tissue distribution and evaluate tumor tracer uptake. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115594/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475550
Series		Accession: GSE115594	ID: 200115594

1926. Targeting CREBBP/EP300 bromodomains in cancer
(Submitter supplied) Changes in gene expression caused by CREBBP/EP300 bromodomain inhibitors in a CML cell line
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110229/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433209
Series		Accession: GSE110229	ID: 200110229

1927. JMJD3 facilitates C/EBPβ-centered transcriptional program to exert oncorepressor activity in AML
(Submitter supplied) JMJD3, a stress-inducible H3K27 demethylase, plays a critical regulatory role in the initiation and progression of malignant hematopoiesis. However, how this histone modifier effects in a cell type-dependent manner remains unclear. Here, we show that in contrast to its oncogenic effect in preleukemia state and lymphoid malignancies, JMJD3 relieves the differentiation-arrest of certain subtypes (such as M2 and M3) of acute myeloid leukemia (AML) cells. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 GPL17021 26 Samples
FTP download: GEO (BIGWIG, BW, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101891/
Series		Accession: GSE101891	ID: 200101891

1928. Mixed-species RNAseq analysis of human lymphoma cell adhesion to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of MCL and CLL patients.
(Submitter supplied) Background:A subset of hematological cancer patients is refractory to treatment or suffer relapse, due in part to minimal residual disease, whereby some cancer cells survive treatment via microenvironment interaction. Cell-adhesion mediated drug resistance is an important mechanism, whereby cancer cells receive survival signals via interaction with e.g. stromal cells. No genome-wide studies of in vitro systems have yet been performed to compare gene expression in different cell subsets within a co-culture and cells grown separately. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL22245 GPL17021 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388663
Series		Accession: GSE99501	ID: 200099501

1929. Enhancer profiling in metastatic cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL20301 GPL16791 72 Samples
FTP download: GEO (BED, BW, MATRIX, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98015/
Series		Accession: GSE98015	ID: 200098015

1930. Enhancer profiling in metastatic cancer [RNA-Seq]
(Submitter supplied) Metastases cause the majority of cancer-related deaths. Yet, the origins of metastatic cancer phenotypes remain poorly understood. Few metastasis-specific driver mutations have been identified [1-3], raising the possibility that metastatic transcriptional programmes may emerge from perturbations in the oncogenic signalling cascades that support the development of primary tumours. Here, using genome-wide histone modification profiling, high-throughput chromatin conformation capture by Hi-C and functional analysis in human-derived metastasis models of renal and breast cancers, we identify transcriptional enhancers that drive metastatic cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 24 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383357
Series		Accession: GSE97928	ID: 200097928

1931. Sequencing-based analyses characterize a tumor suppressive role of mir-1271 repressed by DNA hypermethylation in gastric cancer
(Submitter supplied) To identify tumor suppressive microRNAs repressed by DNA hypermethylation in gastric cancer (GC), we analyzed methylome and miRNome of EpCAM+/CD44+ GC cells. Among a set of microRNAs hypermethylated and downregulated in GC, mir-1271 was uncovered as a microRNA repressed by DNA hypermethylation in GC. Forced expression of mir-1271 significantly suppressed growth, migration, and invasion of GC cells both in vitro and in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 19 Samples
FTP download: GEO (BEDGRAPH, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87785/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA347596
Series		Accession: GSE87785	ID: 200087785

1932. Targeting CREBBP/EP300 in cancer
(Submitter supplied) Antiprolifereative effects of CREBBP/EP300 inhibitors were tested in human leukemia and lymphoma cell lines and the molecular mechanisms responsible for such effects were explored.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77295/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309980
Series		Accession: GSE77295	ID: 200077295

1933. Regulatory network controlling tumor-promoting inflammation in human cancers
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL9115 GPL11154 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115599/
Series		Accession: GSE115599	ID: 200115599

1934. Regulatory network controlling tumor-promoting inflammation in human cancers [RNA-seq]
(Submitter supplied) Using an inducible, inflammatory model of breast cellular transformation, we describe the transcriptional regulatory network mediated by STAT3, NF-kB, and AP-1 factors on a genomic scale.  These regulators form transcriptional complexes that directly regulate the expression of hundreds of genes in oncogenic pathways, such as cell proliferation, metastasis, angiogenesis, apoptosis and metabolism, via a positive feedback loop. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115598/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475554
Series		Accession: GSE115598	ID: 200115598

1935. The interplay between SOX4 and SMAD3 in the context of breast cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.  The experiments are described in 2 papers: PMID 30137431 and PMID 30507376
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 50 Samples
FTP download: GEO (BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104761/
Series		Accession: GSE104761	ID: 200104761

1936. Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [Chromium 10X]
(Submitter supplied) Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103867/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407353
Series		Accession: GSE103867	ID: 200103867

1937. Single cell analysis reveals cancer cell heterogeneities in hepatocellular carcinoma [SMART-seq]
(Submitter supplied) Combined transcriptomic and functional analyses of HCC cells at single-cell level were performed to assess CSC heterogeneity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 138 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103866/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407354
Series		Accession: GSE103866	ID: 200103866

1938. Single cell analysis reveals cancer cell heterogeneities in hepatcellular carcinoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 141 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103591/
Series		Accession: GSE103591	ID: 200103591

1939. CARM1/PRMT4 is essential for myeloid leukemogenesis but dispensable for normal hematopoiesis
(Submitter supplied) We investigated the role of PRMT4 in normal and malignant hematopoiesis. We found that knockdown of PRMT4 impairs cell cycle progression, induces apoptosis, and downgretulateds E2F target genes in leukemia cell lines, identifying several mechanisms for the leukemia-specific dependence on PRMT4.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103528/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401819
Series		Accession: GSE103528	ID: 200103528

1940. Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation
(Submitter supplied) Histone H2B monoubiquitylation (H2Bub1) is localized to transcribed regions of genes and spread in parallel with the progress of RNA polymerase II (Pol II). H2Bub1 levels are highly correlated both with transcription and elongation rates of mammalian genes. Although H2Bub1 correlate with elongation rates, it is not clear whether the correlation is due to causative role of H2Bub1 in regulating elongation rate or the vice versa. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69738/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286307
Series		Accession: GSE69738	ID: 200069738

1941. mRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis
(Submitter supplied) Treatment of neuroepithelial cancers remains a daunting clinical challenge, particularly due to an inability to address rampant invasion deep into eloquent regions of the brain. Given the lack of access, and the dispersed nature of brain tumor cells, we explore the possibility of electric fields inducing directed tumor cell migration. In this study we investigate the properties of populations of brain cancer undergoing electrotaxis, a phenomenon whereby cells are directed to migrate under control of an electrical field. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115509/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA475228
Series		Accession: GSE115509	ID: 200115509

1942. Histone Variant H2A.Z Defines Cell Identity in Vascular Smooth Muscle Cells as Revealed by Single-Cell Transcriptomics
(Submitter supplied) We applied single-cell RNA-Seq to analyze human diseased arteries, and identified histone variant H2A.Z as a key histone signature to maintain vascular smooth muscle cell (VSMC) identity. We show that H2A.Z occupies genomic regions near VSMC marker genes and its occupancy is decreased in VSMC undergoing dedifferentiation. Mechanistically, H2A.Z occupancy preferentially promotes nucleosome turnover, facilitates the recruitment of Smad3 and Med1 to VSMC marker genes, thereby activating gene expression. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 52 Samples
FTP download: GEO (BIGWIG, CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112417/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445961
Series		Accession: GSE112417	ID: 200112417

1943. Transcriptional responses of melanoma cells to BRAF inhibition
(Submitter supplied) We performed a time-course experiment to determine the temporal transcriptional changes that occur in human melanoma cells when cultured with the BRAF inhibitor vemurafenib from 3 days to 73-90 days.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110054/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432707
Series		Accession: GSE110054	ID: 200110054

1944. Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma
(Submitter supplied) MYC genes are frequently amplified and correlate with poor prognosis in MB. BET bromodomains recognize acetylated lysine residues and often promote and maintain MYC transcription. Certain cyclin-dependent kinases (CDKs) are further known to support MYC stabilization in tumor cells. In this report, MB cells were suppressed by combined targeting of MYC expression and MYC stabilization using BET bromodomain inhibition and CDK2 inhibition, respectively. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17301 GPL16331 50 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420018
Series		Accession: GSE107405	ID: 200107405

1945. Persistence of stem cell metabolism in cancers as a failure of differentiation
(Submitter supplied) Tumor glucose uptake was measured by FDG-PET in 859 patients with histologically diverse cancers. We used normal mixture modeling to explore FDG-PET standardized uptake values (SUV) distributions and tested for association between glucose uptake and histological differentiation, risk of lymph node metastasis, and survival. Using RNA-seq data, we performed pathway and transcription factor analyses to compare tumors with high and low levels of glucose uptake. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99790/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389596
Series		Accession: GSE99790	ID: 200099790

1946. Next Generation Sequencing Facilitates Quantitative Analysis of ALDH+ E-BCSC, CD24-CD44+ M-BCSC and Bulk tumor cell Transcriptomes from MC1 and Vari068 PDX models of TNBC
(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of genes in E-, M-BCSCs and bulk tumor cells in two PDX models of triple negative breast cancer .
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115302/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA474498
Series		Accession: GSE115302	ID: 200115302

1947. DHX15 regulates CMTR1-dependent gene expression and cell proliferation
(Submitter supplied) We discovered that the RNA helicase DHX15 is a regulator of the methyltransferase CMTR1.  To determine the biological consequences of this interaction we overexpressed CMTR1 or a mutated CMTR1 (2LA)that does not bind DHX15, in the human breast cancer cell line HCC1806.  To assess the effects of the DHX15-CMTR1 interaction on translation, polysomes were separated on a sucrose gradient and sequencing libraries generated from the polysomal and input RNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113573/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453131
Series		Accession: GSE113573	ID: 200113573

1948. A compendium of long non-coding RNAs transcriptional fingerprint in multiple myeloma
(Submitter supplied) Multiple myeloma (MM) is a malignant proliferation of bone marrow plasma cells (PCs) characterized by highly heterogeneous genetic background and clinical course, and whose pathogenesis remains largely unknown. Long ncRNAs (lncRNAs) are a large class of non-protein-coding RNA, involved in many physiological cellular and genomic processes as well as in carcinogenesis, cancer metastasis and invasion. Although still in its infancy, the knowledge of the role of lncRNAs in MM is progressively expanding. Besides studies on selected candidates, lncRNAs expression at genome-wide transcriptome level is confined to microarray technologies, thus investigating a limited collection of transcripts.  Herein, we assessed the lncRNAs expression profiling by RNA-sequencing in a cohort of 30 MM patients, aimed at defining a comprehensive catalogue of lncRNAs specifically associated with the main MM molecular subgroups and genetic alterations. We identified 391 deregulated lncRNAs, 67% of which were also detectable and validated by whole-transcript microarrays. In addition, we identified a list of lncRNAs, with potential relevance in MM, co-expressed and in close proximity to genes that might undergo a cis-regulatory relationship.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109342/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430521
Series		Accession: GSE109342	ID: 200109342

1949. Genomic and Epigenomic Signatures of Platinum Re-sensitization in ovarian cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by genome tiling array
Platforms: GPL13534 GPL11154 238 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102120/
Series		Accession: GSE102120	ID: 200102120

1950. Genomic signatures of platinum re-sensitization in ovarian cancer [RNA-Seq]
(Submitter supplied) Epigenetic changes, particularly DNA methylation aberrations have been implicated in acquired resistance to platinum in ovarian cancer. A multi-institutional randomized clinical trial compared a regimen of a DNA methyl transferase (DNMT) inhibitor guadecitabine and carboplatin to physician’s choice chemotherapy for patients with recurrent platinum resistant ovarian cancer. Tumor biopsies or malignant ascites were collected at day 1 of cycle 1 (pre-guadecitabine) and after two cycles of treatment (post-decitabine). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 92 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102118/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396733
Series		Accession: GSE102118	ID: 200102118

1951. ChIP-Seq and CAGE profiling of cell lines
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 64 Samples
FTP download: GEO (BED, BROADPEAK, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113715/
Series		Accession: GSE113715	ID: 200113715

1952. CAGE profiling after treatment with JQ1 BET inhibitor in lung cancer cell line.
(Submitter supplied) The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113711/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453767
Series		Accession: GSE113711	ID: 200113711

1953. Transcriptional profiling of HT-29 cells with different treatments
(Submitter supplied) Through RNA-seq, we investigated the transcriptional changes of necroptotic cell induced by TNF-α, SM-164 and zVAD. We report here that necroptosis leads to transcriptional activation of a large set of genes including pro-inflammatory cytokines, which is much stronger than that triggered by TNF-α alone. Furthermore, the robust induction of cytokine expression could be blocked by necroptotic inhibitor Nec-1s. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21697 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108621/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427878
Series		Accession: GSE108621	ID: 200108621

1954. RNA-sequencing and MeDIP-sequencing of shSRC-1 and shNT tamoxifen treated LY2 cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99649/
Series		Accession: GSE99649	ID: 200099649

1955. RNA-sequencing of shSRC-1 and shNT tamoxifen treated LY2 cells
(Submitter supplied) The steroid co-activator protein SRC-1 plays an important role in endocrine therapy resistant breast cancer. Its expression is associated with large high grade tumours, HER2 positivity, disease recurrence and resistance to endocrine therapy. SRC-1's role in affecting the transcriptome of the breast cancer endocrine resistant setting is uncovered through this RNA-seq analysis of LY2 cells grown with or without the presence of SRC-1
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99647/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389214
Series		Accession: GSE99647	ID: 200099647

1956. A Unique B-cell Regulome links Notch to Downstream Oncogenic Pathways in Small B-cell Lymphoma
(Submitter supplied) We perform integrative analysis of Notch-dependent transcripts, genome-wide binding of Notch transcription complex subunits, and enhancer-promoter interactions to identify direct Notch target genes, including the oncogene MYC, and validate their relevance to mantle cell lymphoma and chronic lymphocytic leukemia in vivo.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL11154 111 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382194
Series		Accession: GSE97541	ID: 200097541

1957. Acid suspends the circadian clock in hypoxia through inhibition of mTOR
(Submitter supplied) Recent reports indicate hypoxia influences the clock through the transcriptional activities of hypoxia inducible factors (HIFs) at clock genes. Unexpectedly, we uncover a profound disruption of the circadian clock and diurnal transcriptome when hypoxic cells are permitted to acidify, recapitulating the tumor microenvironment. Buffering against acidification or inhibiting lactic acid production fully rescues circadian oscillation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396153
Series		Accession: GSE101988	ID: 200101988

1958. Oncogenic properties of NEAT1 in prostate cancer cells depend on the CDC5L-AGRN transcriptional regulation circuit
(Submitter supplied) Silencing NEAT1 in prostate cancer cells repressed the transcriptional activity of CDC5L, and RNA-seq and  further analyses revealed a handful of potential targets of CDC5L regulated by NEAT1 expression. We have established the requirement of the CDC5L-AGRN circuit for the essential oncogenic role of NEAT1 in prostate cancer cells. Here we provide processed raw counts files.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114959/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473338
Series		Accession: GSE114959	ID: 200114959

1959. RNA expression following TMPRSS11B overexpression or depletion
(Submitter supplied) Purpose: We are analyzing differential gene expression in human bronchial epithelial cells with TMPRSS11B overexpression or control GFP, as well has human lung squamous cell cancer line HCC2814 with inducible knockdown of TMPRSS11B or control.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473063
Series		Accession: GSE114850	ID: 200114850

1960. In-Vivo Expansion of Cancer Stemness Affords Novel Cancer Stem Cell Targets: Malignant Rhabdoid Tumor as an Example
(Submitter supplied) Cancer stem cell (CSC) identification relies on transplantation assays of cell sub-populations sorted from fresh tumor samples. Herein, we attempt to bypass limitations of abundant tumor source and predetermined immune selection by in-vivo propagating patient derived xenografts (PDX) from human malignant rhabdoid tumor (MRT), a rare and lethal pediatric neoplasm, to an advanced state in which most cells behave as CSCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114471/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471507
Series		Accession: GSE114471	ID: 200114471

1961. Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of leukemia cell line MOLM-13 cells
(Submitter supplied) To explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in leukemia cell line MOLM-13 cells and performed RNA-seq experiments to profile transcriptional changes upon FIS1 depletion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464347
Series		Accession: GSE114111	ID: 200114111

1962. Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells
(Submitter supplied) To explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in primary human AML cells and performed RNA-seq experiments to profile global gene expression changes upon FIS1 depletion.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114109/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464346
Series		Accession: GSE114109	ID: 200114109

1963. Mitochondrial Fission 1 (FIS1) knockdown effect on the H3K27Ac status of leukemia cell line MOLM-13 cells
(Submitter supplied) To examine if loss of FIS1 would alter the H3K27Ac status of leukemic cells, we used shRNA to knock down the expression of FIS1 in leukemic cell line MOLM-13 cells and performed H3K27Ac CHIP-seq to characterize any changes in the H3K27Ac marks upon loss of FIS1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464339
Series		Accession: GSE114106	ID: 200114106

1964. Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 (PRKAA1) knockdown effect on the transcriptome of primary human acute myeloid leukemia (AML) cells
(Submitter supplied) To explore the function of AMPK signaling in acute myeloid leukemia (AML), we used shRNA to knock down the expression of PRKAA1, the catalytic subunit of the 5'-prime-AMP-activated protein kinase (AMPK), in primary human AML cells and performed RNA-seq experiment to profile transcriptional changes upon AMPK inactivation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114105/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA464341
Series		Accession: GSE114105	ID: 200114105

1965. RNA-seq from HNSCC and melanoma populations
(Submitter supplied) Populations were sorted from tumor speciments via flow cytometry using EPCAM, FAP, CD45, and CD31 surface markers
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 106 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113839/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454219
Series		Accession: GSE113839	ID: 200113839

1966. Clinically-relevant cell type cross-talk identified from a lung tumor microenvironment interactome
(Submitter supplied) Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. To develop a deeper understanding of the interactions between cells within human lung tumors we performed RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17553 185 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111907/
Series		Accession: GSE111907	ID: 200111907

1967. Inhibition of microRNA-138 enhances bone formation in multiple myeloma bone marrow niche
(Submitter supplied) Myeloma bone disease is a devastating complication of multiple myeloma (MM) and is caused by dysregulation of bone remodeling processes in the bone marrow microenvironment. Previous studies showed that microRNA-138 (miR-138) is a negative regulator of osteogenic differentiation of mesenchymal stromal cells (MSCs) and that inhibiting its function enhances bone formation in vitro. In this study, we explored the role of miR-138 in myeloma bone disease and evaluated the potential of systemically delivered locked nucleic acid (LNA)-modified anti-miR-138 oligonucleotides in suppressing myeloma bone disease. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437669
Series		Accession: GSE111651	ID: 200111651

1968. An integrative network biology analysis identifies miR-508-3p as the determinant and a prognosis biomarker of the mesenchymal subtype ovarian cancer
(Submitter supplied) Recently, several research groups have identified the mesenchymal subtype of serous OvCa on the basis of transcriptome data and its potential correlation with poor prognosis. We set out to define the regulatory mechanisms underlying the distinct gene expression profiles of serous OvCa using a network-based approach involving multiple molecular modalities such as gene expression and microRNA (miR) expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428968
Series		Accession: GSE108863	ID: 200108863

1969. Next Generation Sequencing  Quantitative Analysis of altered expression of genes in lncRNA LNMAT1 knockdown bladder cancer cells
(Submitter supplied) Bladder cancer is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. LNMAT1 is reported to play diverse roles in the development and progression of human cancer. However, its function and underlying mechanism in bladder cancer remains unclear. The goal of this study is to identify the target genes of LNMAT1 in bladder cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106637/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417490
Series		Accession: GSE106637	ID: 200106637

1970. Long noncoding RNA LNMAT1 promotes lymphatic metastasis in bladder cancer
(Submitter supplied) Long non-coding RNAs (lncRNAs) are a large class of non-protein-coding transcripts that are over 200nt in length. LncRNAs have emerged as key regulator of biological process involved in the development and progression of bladder cancer. Bladder cancer is one of the most common genitourinary malignancies worldwide, with approximately 429,800 new cases and 165,100 deaths annually in the world. To identify critical lncRNAs that contributes to the progression of bladder cancer, Next generation sequencing (NSG) was performed in five paired high-grade muscle invasive bladder cancer (MIBC) and normal adjacent tissues (NAT), and in five lymph node (LN)-positive and LN-negative bladder cancer tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106534/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417154
Series		Accession: GSE106534	ID: 200106534

1971. Salmonella activation of STAT3 signaling by SarA effector promotes intracellular replication and production of IL-10
(Submitter supplied) Salmonella enterica is an important foodborne pathogen that utilizes secreted effector proteins to manipulate host pathways to facilitate survival and dissemination. Different S. enterica serovars cause disease syndromes ranging from self-limited gastroenteritis to typhoid fever and vary in their repertoire of effectors. We leveraged this natural diversity to identify stm2585, here designated sarA (Salmonella anti-inflammatory response activator), as a Salmonella effector secreted primary by the SPI-2 type III secretion system. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104354/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412406
Series		Accession: GSE104354	ID: 200104354

1972. Transcript expression of microdissected xenografted glioblastomas with and without treatment with Lck-I
(Submitter supplied) Migration of human glioma stem cells (hGSCs) within the brain parenchyma makes glioblastoma one of the most aggressive and lethal tumors. Studies of the cellular and molecular mechanisms underlying hGSC migration are hindered by the limitations of existing migration models. Here we developed a dorsal root ganglion axon-oligodendrocyte-hGSC co-culture to study in real time the migration and interaction of hGSCs with their microenvironment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95289/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376570
Series		Accession: GSE95289	ID: 200095289

1973. Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome variation profiling by array
Platforms: GPL18336 GPL11154 GPL9115 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55383/
Series		Accession: GSE55383	ID: 200055383

1974. Integrative Analysis of Tamoxifen-resistant Cell Line Models Based on Sequencing Genomes, Transcriptomes and Epigenomes [seq]
(Submitter supplied) Purpose: Tamoxifen is the most commonly used antiestrogen drug for breast cancer treatment, however, acquired resistance is a considerable challenge in clinic. Complexity and redundancy in biological system implies tamoxifen resistance is associated with complex biological processes. The aim of this study is to attempt to reveal the mechanism of tamoxifen resistance using high-throughput sequencing technique. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 26 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55343/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA239371
Series		Accession: GSE55343	ID: 200055343

1975. Predicting Neuroblastoma Using Developmental Signals and a Logic-Based Model
(Submitter supplied) Genomic information from human patient samples of pediatric neuroblastoma cancers and known outcomes have led to specific gene lists put forward as high risk for disease progression. However, the reliance on gene expression correlations rather than mechanistic insight has shown limited potential and suggests a critical need for molecular network models that better predict neuroblastoma progression. In this study, we construct and simulate a molecular network of developmental genes and downstream signals in a 6-gene input logic model that predicts a favorable/unfavorable outcome based on the outcome of the four cell states including cell differentiation, proliferation, apoptosis, and angiogenesis. We simulate the mis-expression of the tyrosine receptor kinases, trkA and trkB, two prognostic indicators of neuroblastoma, and find differences in the number and probability distribution of steady state outcomes. We validate the mechanistic model assumptions using RNAseq of the SHSY5Y human neuroblastoma cell line to define the input states and confirm the predicted outcome with antibody staining. Lastly, we apply input gene signatures from 77 published human patient samples and show that our model makes more accurate disease outcome predictions for early stage disease than any current neuroblastoma gene list. These findings highlight the predictive strength of a logic-based model based on developmental genes and offer a better understanding of the molecular network interactions during neuroblastoma disease progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115166/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473995
Series		Accession: GSE115166	ID: 200115166

1976. The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 124 Samples
FTP download: GEO (BROADPEAK, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108028/
Series		Accession: GSE108028	ID: 200108028

1977. The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [RNA-Seq Tumor]
(Submitter supplied) Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate a SS transcriptional signature we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108027/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422265
Series		Accession: GSE108027	ID: 200108027

1978. The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [RNA-Seq Cell]
(Submitter supplied) Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate a SS transcriptional signature we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108026/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422264
Series		Accession: GSE108026	ID: 200108026

1979. JAK2 is dispensable for maintenance of JAK2 mutant B-cell acute lymphoblastic leukemias
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL18573 21 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102535/
Series		Accession: GSE102535	ID: 200102535

1980. Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization 
(Submitter supplied) In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL18573 GPL11154 45 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101921/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395931
Series		Accession: GSE101921	ID: 200101921

1981. CDK4/6 inhibitor resistance in prostate cancer
(Submitter supplied) CDK4/6 kinase inhibitors have shown great promise in clinical trials in various cancer types and have recently entered clinical trial for advanced prostate cancer. Although patients are expected to respond well to this class of drugs, development of resistance in some patients is anticipated. To pre-empt this and study how prostate cancer may evade CDK4/6 inhibition, new resistance models were generated from LNCaP and LAPC4 prostate cancer cells cells by prolonged culturing in presence of 0.5uM palbociclib. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99675/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389297
Series		Accession: GSE99675	ID: 200099675

1982. Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13
(Submitter supplied) The constitutively active androgen receptor (AR) splice variant 7 (AR-V7) plays an important role in the progression of castration-resistant prostate cancer (CRPC). Although biomarker studies established the role of AR-V7 in resistance to AR-targeting therapies, how AR-V7 mediates genomic functions in CRPC remains largely unknown. Using a ChIP-exo approach, we show AR-V7 binds to distinct genomic regions and recognizes a full-length androgen-responsive element in CRPC cells and patient tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL20301 GPL11154 40 Samples
FTP download: GEO (BEDGRAPH, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99378/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388315
Series		Accession: GSE99378	ID: 200099378

1983. Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
4 related Platforms 267 Samples
FTP download: GEO (BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97669/
Series		Accession: GSE97669	ID: 200097669

1984. Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and PVT1 Knockdown by CRISPRi in MDA-MB-231 human breast cancer cell line
(Submitter supplied) Induced MYC expression by CRISPRi targeting PVT1 was validated by RNA-seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97587/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382390
Series		Accession: GSE97587	ID: 200097587

1985. The transition from proliferation to quiescence in glioblastoma stem-like cells requires Ca2+ signaling and mitochondria remodeling
(Submitter supplied) Quiescence is a reversible cell-cycle arrest used by Cancer Stem Cells (CSCs) to evade killing following conventional therapies. Quiescent CSCs are therefore one of the main cause of cancer recurrence. In glioblastoma, the most common and aggressive primary brain tumors, the quiescent glioblastoma stem-like cells (GSCs) are localized in hypoxic and acidic microenvironments and microenvironmental changes can control cell cycle re-entering of the GSCs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93991/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363017
Series		Accession: GSE93991	ID: 200093991

1986. Single-cell RNA-seq analysis of human tumor ascites dendritic cells and macrophages
(Submitter supplied) We performed single-cell RNA-seq on dendritic cells and macrophages isolated from the tumor ascites of one cancer patient. We used the 10x chromium technology. The expression matrix provided in supplementary is the result Cellranger aggregate method on : GSE115007, GSE115006 and GSE103544.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE115nnn/GSE115007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473508
Series		Accession: GSE115007	ID: 200115007

1987. PTHrP overexpression in MCF7 cells
(Submitter supplied) A PTHrP construct expressing full-length secreted PTHrP (-36-139aa) was stably expressed in MCF7 cells. The goal of the study was to determine the gene targets of PTHrP in human MCF7 breast cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110713/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434402
Series		Accession: GSE110713	ID: 200110713

1988. Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 62 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110611/
Series		Accession: GSE110611	ID: 200110611

1989. Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 130d)
(Submitter supplied) Introduction of brain tumor-relevant genetic aberrations initiates different subtypes of brain tumor-like neoplasms in cerebral organoids
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 36 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434108
Series		Accession: GSE110610	ID: 200110610

1990. SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression [sequencing]
(Submitter supplied) Acute lymphoblastic leukemia (ALL) is associated with significant morbidity and mortality necessitating further improvements in diagnosis and therapy.  Targeted therapies directed against epigenetic regulators, which are frequently mutated or misregulated in acute leukemia, are emerging as candidate approaches in preclinical studies and early trials.  However, the epigenetic factors involved in most ALLs are not well defined or functionally characterized. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL21290 22 Samples
FTP download: GEO (BEDGRAPH, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102947/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399516
Series		Accession: GSE102947	ID: 200102947

1991. Targeted mutagenesis recapitulates brain tumor initiation in cerebral organoids (RNA-seq data set: 45d)
(Submitter supplied) Introduction of brain tumor-relevant genetic aberrations initiates different subtypes of brain tumor-like neoplasms in cerebral organoids
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 26 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101577/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394872
Series		Accession: GSE101577	ID: 200101577

1992. IMP3 regulated gene expression in breast cancer cells
(Submitter supplied) IMP3 (IGF2-mRNA binding protein 3) is a member of a family of IGF2-mRNA binding proteins that function in RNA stabilization, trafficking and localization.  It exhibits the properties of an oncofetal protein and its expression correlates with the aggressive behavior of many tumors.  In breast cancer, IMP3 is associated with the highly aggressive triple-negative subtype (TNBC) The challenge is to identify specific proteins and functions that are regulated by IMP3. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107564/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420696
Series		Accession: GSE107564	ID: 200107564

1993. Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18573 26 Samples
FTP download: GEO (BEDGRAPH, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81487/
Series		Accession: GSE81487	ID: 200081487

1994. Gene expression profiling study by RNA-seq for identifying genes associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors
(Submitter supplied) Treatment with ALK tyrosine kinase inhibitors often elicits profound initial antitumor responses in ALK fusion-positive patients with lung adenocarcinoma. However, patients invariably develop acquired resistance to ALK inhibitors. In this study, we aimed to identify molecular events that limit the response to ALK inhibition using genetic and epigenetic approaches. To identify novel mechanisms of acquired resistance to ALK inhibitors, we established in vitro models of acquired resistance to ceritinib using H3122 cell. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81484/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321747
Series		Accession: GSE81484	ID: 200081484

1995. Resetting the Epigenetic Balance of Polycomb/COMPASS Function at Enhancers for Cancer Therapy
(Submitter supplied) MLL3/KMT2C is a COMPASS family member and tumor suppressor that functions as a histone H3K4 mono-methyltransferase at enhancers. Human cancer genome sequencing studies have identified frequent MLL3 point mutations, however, the question of how these mutations alter MLL3 function and contribute to oncogenesis remains unanswered. Here, we have characterized a cancer mutational hot spot in the MLL3 Plant Homeo Domain (PHD) repeats that correlates with poor patient survival. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 110 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381421
Series		Accession: GSE97326	ID: 200097326

1996. Adipocyte-derived lipids mediate melanoma progression via FATP proteins
(Submitter supplied) We performed RNA-seq on A375 melanoma cells in monoculture or after coculture with adipocytes and identified differentially expressed genes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114941/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473164
Series		Accession: GSE114941	ID: 200114941

1997. Transcriptome analysis of the glioma stem cells  infected with ZIKV
(Submitter supplied) Glioma stem cells derived from patient samples were infected with ZIKV at MOI of 1 for 48hrs, total RNA was extracted and deep sequenced to compare the gene expression  profiles between mock and ZIKV infected cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20795 6 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114907/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA473149
Series		Accession: GSE114907	ID: 200114907

1998. RNA-sequencing of isogenic primary, pre-malignant immortalized, and Ras-transformed human mammary epithelial cells
(Submitter supplied) Understanding changes in gene expression during tumor initiation and progression is critical to understanding how genetic alterations drive malignancy. We used a genetically defined cell culture model to study the progression of normal human mammary epithelial cells (HMECs) to malignancy. Primary HMECs were immortalized through the expression of hTERT, p53DD, cyclin D1, CDK4R24C and c-MYCT58A. This immortalization conferred limitless replicative potential as well as migratory capacity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110677/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434238
Series		Accession: GSE110677	ID: 200110677

1999. Early response of human ovarian and fallopian tube surface epithelial cells to norepinephrine
(Submitter supplied) The purpose of this study is to understand the effects of adrenergic signaling on the transcriptome of cell line models postulated to be the cells of origin of epithelial ovarian cancers using RNA-Seq. Here we explored the effects of the stress-related hormone, norepinephrine, on normal human ovarian and fallopian tube surface epithelial cellss. We investigated the early transcriptional response to norepinephrine in normal immortalized ovarian surface epithelial cells and fallopian tube secretory cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108084/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422427
Series		Accession: GSE108084	ID: 200108084

2000. RNAseq of Breast cancer PDX samples
(Submitter supplied) RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 125 Cycle Paired-End Sequencing v4
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451206
Series		Accession: GSE113476	ID: 200113476

