
2001. Single cell RNA sequencing of multiple myeloma II
(Submitter supplied) To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By combining allele frequency and expression magnitude deviations, HoneyBADGER is able to infer the presence of subclone-specific alterations in individual cells and reconstruct subclonal architecture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 174 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110499/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433864
Series		Accession: GSE110499	ID: 200110499

2002. Global hypomethylation mediated changes regulate constitutive PD-L1 expression in melanoma
(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: GPL16791 24 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107622/
Series		Accession: GSE107622	ID: 200107622

2003. Global hypomethylation mediated changes regulate constitutive PD-L1 expression in melanoma [RNA-Seq]
(Submitter supplied) PD-L1 is a ligand for the inhibitory PD1 receptor on T cells and its expression in some cancers inhibits anti-cancer immune response. In melanoma, PD-L1 expression is induced in response to immune stimuli but in a proportion of melanomas it is constitutively expressed. Factors that drive constitutive expression of PD-L1 are unknown. Here we performed RNA-Seq analysis of six cell lines that constitutively express PD-L1 (PD-L1 positive, referred to as PD-L1CON) and six cell lines that only express PD-L1 after treatment with IFN- (PD-L1 negative, referred to as PD-L1IND)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420861
Series		Accession: GSE107620	ID: 200107620

2004. Chromatin binding profiles of the APC tumor suppressor and changes in gene expression following APC silencing
(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 GPL9115 7 Samples
FTP download: GEO (FASTA, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99264/
Series		Accession: GSE99264	ID: 200099264

2005. Gene expression data from the HCT-116 colon cancer cell line in the presence or absence of siRNA targeting APC
(Submitter supplied) Gene expression data were collected by RNA-seq from HCT-116 cells in the presence or absence of siRNA targeting APC and 1,376 transcripts changed in expression following APC silencing were identified relative to scrambled siRNA-transfected and untreated controls.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99263/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388012
Series		Accession: GSE99263	ID: 200099263

2006. Dual inhibition of HDMX and HDM2 as a Therapeutic Strategy in Leukemia
(Submitter supplied) The p53 protein is the most frequently inactivated tumor suppressor in human cancer. While p53 mutations are found in 50% of all cancers, the p53 pathway can also be suppressed by its interaction with endogenous inhibitors HDMX and HDM2, which are frequently overexpressed in patients with acute myeloid leukemia and other cancers. Thus, pharmacological disruption of both these interactions is an attractive strategy to restore p53-dependent tumor suppressor activity in AML with wild type P53. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TAB, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99255/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387730
Series		Accession: GSE99255	ID: 200099255

2007. RNA transcriptome sequencing analysis of AGS cells transfected with MFAP2 shRNA or control shRNA
(Submitter supplied) An RNA transcriptome sequencing analysis was performed in AGS cells that were transfected with MFAP2 shRNA or control shRNA.
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/GSE114nnn/GSE114796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472638
Series		Accession: GSE114796	ID: 200114796

2008. Differential gene expression tools exhibit substandard performance for long non-coding RNA-sequencing data
(Submitter supplied) Paired End PolyA-+ RNA-sequencing of NGP cells with and without NGP treatment in 10 replicates.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104756/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413772
Series		Accession: GSE104756	ID: 200104756

2009. B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL17556 GPL11154 12 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100112/
Series		Accession: GSE100112	ID: 200100112

2010. Comparison of rectal patient data separated by their event of developing distant metastasis
(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: GPL23593 GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100110/
Series		Accession: GSE100110	ID: 200100110

2011. Comparison of rectal patient data separated by their event of developing distant metastasis [RNA-Seq]
(Submitter supplied) The rectal cancer patient data set consists of 10 patients from a clinical study at the Surgery department of the University Medical Center Göttingen collected over a longer time. Patients were chosen based on the follow-up time and development of a distant metastasis. First a balanced sample size of five versus five patients with and without  a metastatic event was chosen. This needed to be changed to six versus four. 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/GSE99nnn/GSE99897/
Series		Accession: GSE99897	ID: 200099897

2012. B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line [RNA-Seq]
(Submitter supplied) RNA-Seq profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hrs . The Burkitt Lymphoma cell line were either only cultured in cell culture medium supplemented with 10 mM HEPES at 1 × 106 cells/ml  or additionally incubated with B-cell activating factor (BAFF) for 24 hrs
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/GSE99nnn/GSE99768/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389572
Series		Accession: GSE99768	ID: 200099768

2013. Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis
(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 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84478/
Series		Accession: GSE84478	ID: 200084478

2014. Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis [human cells]
(Submitter supplied) Pulmonary Lymphangioleiomyomatosis (LAM), a rare lung disease that affects predominantly women, is characterized by proliferation of smooth muscle-like cells in the lungs, destruction of lung tissue, upregulation of VEGF-D, and growth of lymphatic vessels inducing a loss of pulmonary function. TSC2 gene mutations that render TSC2 inactive are a common finding associated with LAM. To better understand the function of the TSC2 gene in LAM , we sought to characterize differences in the transcriptome of cells where TSC2 is inactivated. 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/GSE84476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329373
Series		Accession: GSE84476	ID: 200084476

2015. Genes regulated by soluble guanylyl cyclase in VCaP prostate cancer cells
(Submitter supplied) The aberrant activation of the ERG oncogenic pathway due to TMPRSS2-ERG gene fusions is the major driver of prostate cancer initiation and progression. We identified the alpha1 and beta1 subunits of soluble guanylyl cyclase (GUCY1A1, GUCY1B1) as major ERG-regulated genes in prostate cancer cells. Soluble guanylyl cyclase (sGC) is the major mediator of nitric oxide signaling in cells that, upon nitric oxide binding, catalyzes the synthesis of cGMP and subsequently activates PKG. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114738/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472401
Series		Accession: GSE114738	ID: 200114738

2016. RNA-sequencing analysis of CD4 T cells following ipilimumab therapy
(Submitter supplied) We sorted CD4 T cells from patients with metastatic melanoma at baseline and after three doses of ipilimumab.
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/GSE114nnn/GSE114716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472360
Series		Accession: GSE114716	ID: 200114716

2017. BRG1 governs Glucocorticoid Receptor interactions with chromatin and pioneer factors across the genome
(Submitter supplied) The Glucocorticoid Receptor (GR) alters transcriptional activity in response to hormones by interacting with chromatin at GR binding sites (GBSs) throughout the genome. Our work in human breast cancer cells identifies three classes of GBSs with distinct epigenetic characteristics and reveals that BRG1 interacts with GBSs prior to hormone exposure. The GBSs pre-occupied by BRG1 are more accessible and transcriptionally active than other GBSs. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL18573 44 Samples
FTP download: GEO (BED, BW, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA447949
Series		Accession: GSE112491	ID: 200112491

2018. Transcriptomic data of MDA-MB-231 cells adapted to culture in media containing different sugars (glucose or fructose) and cultured as mammospheres
(Submitter supplied) We report the single-cell RNA sequencing data obtained from MDA-MB-231 breast cancer cells cultured in standard DMEM with 25 mM glucose, or adapted to culture in DMEM with 10 mM fructose to reduce glycolysis, and then cultured as mammospheres
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/GSE106nnn/GSE106202/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415913
Series		Accession: GSE106202	ID: 200106202

2019. A transcriptionally und functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small cell lung cancer treated with PD-1 blockade
(Submitter supplied) Evidence from mouse chronic viral infection models suggests that CD8+ T cell subsets characterized by distinct expression levels of the receptor PD-1 diverge in their state of exhaustion and potential for reinvigoration by PD-1 blockade. However, it remains unknown whether T cells in human cancer adopt a similar spectrum of exhausted states based on PD-1 expression levels. We compared transcriptional, metabolic, and functional signatures of intratumoral CD8+ T lymphocyte populations with high (PD-1T), intermediate (PD-1N) and no PD-1 expression (PD-1-) from non-small cell lung cancer patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 37 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99531/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388717
Series		Accession: GSE99531	ID: 200099531

2020. Itraconazole targets cell cycle heterogeneity in colorectal cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 80 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114014/
Series		Accession: GSE114014	ID: 200114014

2021. Identifying the molecular mode of action of itraconazole in colorectal cancer
(Submitter supplied) Two cell lines (HT55 and SW948) were found responsive to itraconazole treatment.  To identify the mode of action cells were treated with itraconazole or control (DMSO) and then subjected to RNAseq analysis once the phenotype had developed
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/GSE114013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454881
Series		Accession: GSE114013	ID: 200114013

2022. Identifying dormant cells in colorectal cancer spheroids
(Submitter supplied) Cellular dormancy and heterogeneous cell cycle lengths provide important explanations for treatment failure following adjuvant therapy with S-phase cytotoxics in colorectal cancer (CRC) yet the molecular control of the dormant versus cycling state remains unknown.  In CRCs dormant cells are found to be highly clonogenic and resistant to chemotherapies.  We sought to understand the molecular features of dormant CRC cells to facilitate rationale identification of compounds to target both dormant and cycling tumour cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 64 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114012/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454879
Series		Accession: GSE114012	ID: 200114012

2023. Gastrointestinal Stromal Tumor Enhancers Support a Transcription Factor Network Predictive of Clinical Outcome
(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 74 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95864/
Series		Accession: GSE95864	ID: 200095864

2024. Gastrointestinal Stromal Tumor Enhancers Support a Transcription Factor Network Predictive of Clinical Outcome
(Submitter supplied) Activating mutations in the KIT or PDGFRA receptor tyrosine kinases are hallmarks of gastrointestinal stromal tumor (GIST). The biological underpinnings of recurrence following resection or disease progression beyond kinase mutation are poorly understood. Utilizing chromatin immunoprecipitation with sequencing (ChIP-seq) of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378618
Series		Accession: GSE95863	ID: 200095863

2025. Comprehensive profiling of translation initiation in influenza-virus infected cells
(Submitter supplied) Cellular stress is often accompanied by non-canonical initiation of translation at alternate start codons in mammalian cells. Here we systematically investigate the extent and impact of alternate translation initiation in the context of influenza virus infection. We use ribosome profiling with the initiation inhibitor lactidomycin to experimentally delineate translation initiation sites in a human lung epithelial cell line infected with influenza virus.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 12 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114636/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA472015
Series		Accession: GSE114636	ID: 200114636

2026. Metabolic reprogramming of Kaposi’s sarcoma associated herpes virus infected B-cells in hypoxia
(Submitter supplied) We report differential gene expression in BJAB-KSHV/BJAB cells treated with Cobalt chloride/BJAB-KSHV cells treated with Cobalt Chloride compared to BJAB cells
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/GSE114nnn/GSE114625/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471994
Series		Accession: GSE114625	ID: 200114625

2027. RNA sequencing of prostate cancer and normal tissue from African Americans and European Americans
(Submitter supplied) Background:African American men (AAM) are at higher risk of being diagnosed with prostate cancer (PCa) and are at higher risk of dying from the disease compared to European American men (EAM). We sought to better understand PCa molecular diversity that may be underlying these disparities. We ran RNA-sequencing data analysis on high-grade PCa to identify genes showing differential tumor versus normal adjacent tissue expression patterns unique to AAM or EAM.
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/GSE104nnn/GSE104131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA411786
Series		Accession: GSE104131	ID: 200104131

2028. Conservative alteration of chromosomal expression pattern across human solid tumor types
(Submitter supplied) We used RNASeq technology to get whole transcription profilings of 2 control samples (MCF7), 2 replicates of MCF7_sh_XIST_1 and 2 replicates of MCF7_sh_XIST_2. Our goal is to find the differentially expressed genes by comparing knockdown of XIST in MCF7 and control MCF7 in Breast cancer 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/GSE99nnn/GSE99048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387133
Series		Accession: GSE99048	ID: 200099048

2029. Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia
(Submitter supplied) Splicing factor SF3B1 is frequently mutated in chronic lymphocytic leukemia (CLL) patients and has been suggested as a potential therapeutic target. In this study, we performed RNA-seq analysis to evaluate the global impact of SF3B1 modulator sudemycin D6 (SD6) on alternative splicing. Our analysis revealed significant increases in global intron-retention in SD6-treated CLL cells. Pathway analysis of the genes associated with increased intron-retention suggested that B-cell receptor (BCR), protein ubiquitination, and PI3K signaling pathways were among the top canonical pathways being affected by SD6. 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/GSE114nnn/GSE114514/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471642
Series		Accession: GSE114514	ID: 200114514

2030. Profiling of tumor-infiltrating CD8 T cells according to their expression status of CD39
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 32 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113590/
Series		Accession: GSE113590	ID: 200113590

2031. Profiling of lung tumor-infiltrating CD8 T cells according to their expression status of CD39
(Submitter supplied) Human tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express unique receptors that can recognize peptides at the host’s cells, including tumor cells. After probing the antigen specificity of ex-vivo tumor-infiltrating CD8 T cells from human tumors, we hypothesized that expression of CD39 was correlated with tumor-specificity. The present experiment aims at better characterizing ex-vivo CD39+ vs CD39- CD8 T cells.
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/GSE113nnn/GSE113588/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453180
Series		Accession: GSE113588	ID: 200113588

2032. Profiling of colorectal tumor-infiltrating CD8 T cells according to their expression status of CD39
(Submitter supplied) Human tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express unique receptors that can recognize peptides at the host’s cells, including tumor cells. After probing the antigen specificity of ex-vivo tumor-infiltrating CD8 T cells from human tumors, we hypothesized that expression of CD39 was correlated with tumor-specificity. The present experiment aims at better characterizing ex-vivo CD39+ vs CD39- CD8 T cells.
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/GSE113nnn/GSE113585/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453183
Series		Accession: GSE113585	ID: 200113585

2033. CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia
(Submitter supplied) We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that  CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL21290 GPL18573 16 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113191/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450401
Series		Accession: GSE113191	ID: 200113191

2034. Leukaemic alteration of IKZF1 primes stemness and malignancy programs in human lymphocytes
(Submitter supplied) We uncovered upregulated stem cell program in leukaemic lymphoblasts of patients with IKZF1 alterations by analyzing the archived gene-expression profiling datasets. We then used a frequent IKZF1 deletion, IK6, as a model via transduction into human primitive haematopoietic cells, followed by xenotransplantation in mice. Immunophenotypically defined stem, pro-B, and immature/mature (IM/M)-B cells were collected from primary recipients for functional assay and transcriptome profiling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112124/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA439382
Series		Accession: GSE112124	ID: 200112124

2035. Differentially expressed genes post knock down of lincDUSP26
(Submitter supplied) Total RNA from V703 and V481 cells (negative control vs KD of lincDUSP) were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs was calculated as FPKM values.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101342/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394016
Series		Accession: GSE101342	ID: 200101342

2036. Total RNA was extracted from three samples of CD33 CAR or control T cells from three different donors
(Submitter supplied) In vivo persistence of chimeric antigen receptor (CAR) T cells correlates with therapeutic efficacy, yet CAR-specific factors that support persistence are not well resolved. Using a CAR containing a single chain variable fragment (scFv) specific for CD33 linked to a 4-1BB and CD3 zeta signaling domain that is currently in advanced clinical trials, we show that CAR-expression, in a ligand-independent manner, alters T cell differentiation during ex vivo expansion. 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/GSE93nnn/GSE93386/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360844
Series		Accession: GSE93386	ID: 200093386

2037. Direct interaction of MYCN and p53 regulate transcriptional responses in 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
Platforms: GPL9115 GPL11154 11 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83328/
Series		Accession: GSE83328	ID: 200083328

2038. Direct interaction of MYCN and p53 regulate transcriptional responses in neuroblastoma [RNA-Seq]
(Submitter supplied) The net transcriptome of a cancer cell is defined by relative levels of transcription factors, activators, suppressors and co-factors. These in turn are controlled by epigenetic, genetic and metabolic restraints. Here we used RNA-Seq, ChIP-qPCR, and ChIP-Seq to determine the impact of MYCN protein levels on p53 and MYCN mediated transcription in neuroblastoma, a p53 wild-type neural crest derived pediatric malignancy. 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/GSE83nnn/GSE83327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325604
Series		Accession: GSE83327	ID: 200083327

2039. Total RNA-seq of cancer cells with inhibition of DNA and/or histone methylation
(Submitter supplied) Endogenous Retroviruses (ERVs) silencing mechanism depend on DNA methylation, heterochromatin conformation and the PRC2 complex. However, extensive maps of ERVs distribution and the associated epigenetic marks have not yet been provided in human cancer cells. Our purpose in this study is to investigate ERVs expression changes after inhibition of DNA and/or histone methylations. Total RNA-seq in human colon cancer HCT116 cells following DNA methylation inhibitor treatment or knockdown of individual H3K9me2/3 histone methyltransferases revealed that about 1,000 of evolutionary young ERVs were predominantly silenced by DNA methylation, whereas about 800 of intermediate age ERVs were silenced by histone methylations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 30 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108177/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422758
Series		Accession: GSE108177	ID: 200108177

2040. Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq; normal samples]
(Submitter supplied) Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube.  Serous tubal intraepithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. 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/GSE114nnn/GSE114493/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471533
Series		Accession: GSE114493	ID: 200114493

2041. Single cell RNA-seq and ATAC-seq of EMT induced by TGFbeta stimulation and Zeb1 overexpression
(Submitter supplied) We report the application of single cell RNA-sequencing using indrop on an HMLE breast cancer cell line that we induced to undergo EMT. We measured 7523 single cells after 8 and 10 days of stimulation with TGFbeta. In addition, we measured 3496 single cells in an engineered HMLE cell line with Dox inducible Zeb1, after 2 days of stimulation with Doxycycline. Finally, we performed ATAC-seq on CD44 sorted HMLE cells after 8 days of stimulation with TGFbeta.
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 (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE114nnn/GSE114397/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471293
Series		Accession: GSE114397	ID: 200114397

2042. Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy NA-seq (time course)  May 15, 2018   approved  TSV
(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 49 Samples
FTP download: GEO (BW, NARROWPEAK, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99183/
Series		Accession: GSE99183	ID: 200099183

2043. Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq (time course)
(Submitter supplied) Purpose: Characterization of mechanism and vulnerability of BET protein dependency in GBM cells.  Methods: ChIP-seq and RNA-seq were performed on GBM cells at different time points following treatment with dBET6, a novel BET protein degrader. The transcriptome responses of parental and JQ1-resistant U87 cells to JQ1 and dBET6 were compared as well.     Result: This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99181/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387481
Series		Accession: GSE99181	ID: 200099181

2044. Selectively targeting bromodomain and extraterminal proteins for degradation as a novel anti-glioblastoma strategy [RNA-seq]
(Submitter supplied) Purpose: Characterization of mechanism and vulnerability of BET protein dependency in GBM cells.  Methods: ChIP-seq and RNA-seq were performed on GBM cells at different time points following treatment with dBET6, a novel BET protein degrader. The transcriptome responses of parental and JQ1-resistant U87 cells to JQ1 and dBET6 were compared as well.     Result: This study reveals crucial functions of BET proteins and provides the rationale and therapeutic merits of targeted degradation of BET proteins by dBET6 in GBM.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99175/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387467
Series		Accession: GSE99175	ID: 200099175

2045. Induction of Prolonged Early G1 Arrest by CDK4/CDK6 Inhibition Reprograms Lymphoma Cells for Durable PI3Kδ Inhibition Through PIK3IP1
(Submitter supplied) The RNA-seq data presented in this study include libraries from Mantle Cell Lymphoma (MCL) tumor cells of 4 patients, Peripheral Blood B Cells from 3 healthy volunteers and JEKO-1 MCL cell lines
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/GSE46nnn/GSE46846/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA202455
Series		Accession: GSE46846	ID: 200046846

2046. RNA transcriptome sequencing analysis of SGC-7901 cells transfected with tcons_00001221 shRNA or control shRNA
(Submitter supplied) An RNA transcriptome sequencing analysis was performed in SGC-7901 cells that were transfected with tcons_00001221 shRNA or control shRNA.
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/GSE114nnn/GSE114360/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA471072
Series		Accession: GSE114360	ID: 200114360

2047. Establishment and characterization of prostate cancer organoids
(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: GPL21290 GPL22678 GPL16791 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113743/
Series		Accession: GSE113743	ID: 200113743

2048. Establishment and characterization of prostate cancer organoids [RNA-seq]
(Submitter supplied) Prostate cancer translational research has been hampered by the lack of comprehensive and tractable models that represent the genomic landscape of clinical disease. Metastatic castrate-resistant prostate cancer (mCRPC) patient derived xenografts (PDXs) recapitulate the genetic and phenotypic diversity of the disease. We sought to establish a representative, preclinical platform of PDX-derived organoids that is experimentally facile for high throughput and mechanistic analysis.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21290 GPL16791 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113741/
Series		Accession: GSE113741	ID: 200113741

2049. ETS1 acts as a tumor suppressor in breast cancer by inhibiting growth-related factors
(Submitter supplied) To characterize the effect of Core regulatory element (CRE) deletion in breast cancer cell line (MDA-MB-231 cells), we performed gene expression RNA-seq analysis for WT and KO (Core Regulatory Element deleted) MDA-MB-231 cells after 0h, 6h and 24h of P/I treatment.
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/GSE106nnn/GSE106634/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417488
Series		Accession: GSE106634	ID: 200106634

2050. RNA-seq and DNA methylation analysis in head and neck cancer cells and cell lines
(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: GPL13534 GPL18460 25 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98811/
Series		Accession: GSE98811	ID: 200098811

2051. RNA-seq of head and neck cancer cell lines
(Submitter supplied) Transcriptome analysis in head and neck cancer cell lines, FaDu and UMSCC47  with and without 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment.
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/GSE98805/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386285
Series		Accession: GSE98805	ID: 200098805

2052. Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia
(Submitter supplied) In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing the surrounding vasculature network. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O2) conditions, we observed that despite being highly similar, the four cell lines responded strikingly different to hypoxia. 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/GSE109nnn/GSE109367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430693
Series		Accession: GSE109367	ID: 200109367

2053. APT1 regulates the asymmetric partitioning of Notch and Wnt signaling during cell division
(Submitter supplied) Asymmetric cell division results in two distinctly fated daughter cells to generate cellular diversity. A major molecular hallmark of an asymmetric division is the unequal partitioning of cell-fate determinant proteins.  We have previously established that growth factor signaling promotes protein depalmitoylation to foster polarized protein localization, which in turns drives migration and metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105486/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415217
Series		Accession: GSE105486	ID: 200105486

2054. Chronophin regulates metabolic and transcriptomic features of glioblastoma stem-like cells
(Submitter supplied) High throughput sequencing of poly-A RNA
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98797/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386264
Series		Accession: GSE98797	ID: 200098797

2055. Activation of the p53-MDM4 regulatory axis defines the anti-tumour response to PRMT5 inhibition through its role in regulating cellular splicing.
(Submitter supplied) Here we describe broad anti-proliferative activity of potent, selective, reversible inhibitors of protein arginine methyltransferase5 (PRMT5) including GSK3326595 in human cancer cell lines representing both hematologic and solid malignancies. Interestingly, PRMT5 inhibition activated the p53 pathway via the induction of alternative splicing of MDM4. The MDM4 isoforms witch and subsequent p53 activation are critical determinants of the response to PRMT5 inhibition suggesting that the integrity of the p53-MDM4 regulatory axis defines a subset of patients that could benefit from treatment with GSK3326595.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 32 Samples
FTP download: GEO (DIFF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428173
Series		Accession: GSE108651	ID: 200108651

2056. Transcriptome sequencing after MAGOHB knockdown in MAGOH-deleted or non-deleted cancer cells
(Submitter supplied) Transcriptome profiling was performed after knocking down MAGOHB in ChagoK1 cells or ChagoK1 cells with ectopic re-expression of MAGOH-V5
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/GSE113nnn/GSE113848/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454264
Series		Accession: GSE113848	ID: 200113848

2057. mRNA-seq Whole Transcriptome Profiling of Fresh Frozen versus Archived Fixed Tissues
(Submitter supplied) Background: The main bottleneck for genomic studies of tumors is the limited availability of fresh frozen (FF) samples collected from patients, coupled with comprehensive long-term clinical follow-up. This shortage could be alleviated by using existing large archives of routinely obtained and stored Formalin-Fixed Paraffin-Embedded (FFPE) tissues. However, since these samples are partially degraded, their RNA sequencing is technically challenging. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113976/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA454715
Series		Accession: GSE113976	ID: 200113976

2058. Simultaneous and systematic analysis of cellular and viral gene expression during Enterovirus 71-induced host shutoff
(Submitter supplied) Enterovirus 71 (EV71) infection causes a profound shutoff of cellular protein synthesis. Deep RNA-sequencing and ribosome profiling were employed to systematically analyze messenger RNA and ribosome-protected RNA in EV71-infected rhabdomyosarcoma cells at progressive time points following infection. The analysis characterized the dynamic transcriptional and translational landscapes of both the virus and host cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401882
Series		Accession: GSE103308	ID: 200103308

2059. RNA-seq of MCF7 cell lines after EPIC1 siRNA knockdown
(Submitter supplied) In an integrated analysis of long noncoding RNA (lncRNA) epigenetic alterations in 6475 tumor samples and 781 cancer cell lines, we characterized the epigenetic landscape for 1,006 epigenetically activated and 1,117 epigenetically silenced lncRNAs across 20 cancer types. Combining bioinformatics analyses and functional validation, we identified epigenetically induced lncRNA 1 (EPIC1) as a potential oncogene. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385394
Series		Accession: GSE98538	ID: 200098538

2060. CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics 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
Platforms: GPL11154 GPL20301 20 Samples
FTP download: GEO (BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101791/
Series		Accession: GSE101791	ID: 200101791

2061. CBFb-SMMHC inhibition triggers apoptosis by disrupting MYC chromatin dynamics in acute myeloid leukemia [RNA-seq]
(Submitter supplied) We recently reported the discovery of a small molecule inhibitor, AI-10-49 which can specially inhibit the protein-protein interaction between RUNX1 tumor suppressor and CBFβ-SMMHC oncogene. We also demonstrated that AI-10-49 can re-establish the RUNX1 transcriptional program in inv(16) cells and can extend the survival of inv(16) leukemic mice. To identify the transcriptional changes associated with AI-10-49, we performed RNA-seq analysis in ME-1 cells [human inv(16) leukemia cell line] treated with AI-10-49.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV, DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101788/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395541
Series		Accession: GSE101788	ID: 200101788

2062. Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition.
(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; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88738/
Series		Accession: GSE88738	ID: 200088738

2063. Cooptation of tandem DNA repeats for the control of epithelial-to-mesenchymal transition [RNA-Seq]
(Submitter supplied) During normal or pathological epithelial-to-mesenchymal transition, epithelium-specific gene expression is shut down, with the DNA-binding factor ZEB1 acting as a master suppressor of epithelial identity. Here, we show that ZEB1 occupies primate-specific tandem repeats (TRs) harboring dozens of copies of its DNA-binding motif and located within genomic loci relevant for epithelial identity. Deletion of one such repeat in a quasi-mesenchymal human cancer cell line induced the reacquisition of epithelial features and phenocopied the effects of ZEB1 gene deletion. 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/GSE88nnn/GSE88735/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348433
Series		Accession: GSE88735	ID: 200088735

2064. Nrf2 regulated genes in A549 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: GPL20301 GPL18573 10 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113522/
Series		Accession: GSE113522	ID: 200113522

2065. Identification of Nrf2 regulated genes by RNA sequencing
(Submitter supplied) The transcription factor Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is activated by the metabolite  itaconate during metabolic reprogramming. Activated Nrf2 then dampens the release of pro-inflammatory  cytokines and type I IFNs in response to toll-like receptor stimulation. If and how Nrf2 affects cytosolic  antiviral sensing and whether this occurs during metabolic reprogramming is currently not known. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451433
Series		Accession: GSE113519	ID: 200113519

2066. Transcriptional changes after overexpression of proliferation drivers in human mammary epithelial cells.
(Submitter supplied) Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of human cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes tested regulate proliferation, many performing in an unexpectedly highly tissue-specific manner. 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/GSE109nnn/GSE109326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430440
Series		Accession: GSE109326	ID: 200109326

2067. Cleavage Factor 25 Deregulation Contributes to Pulmonary Fibrosis through Alternative Polyadenylation
(Submitter supplied) The purpose of this experiment is to identify the APA targets of CFIm25 in human lung fibroblasts.   Following the knockdown of CFIm25 in normal human lung fibroblasts, we identified 808 genes with shortened 3’UTRs, including those involved in the transforming growth factor-beta signaling pathway, the Wnt signaling pathway, and cancer pathways.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108352/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423249
Series		Accession: GSE108352	ID: 200108352

2068. Polyol pathway links glucose metabolism to the aggressiveness of cancer cells
(Submitter supplied) Cancer cells alter their metabolism to support their malignant properties. By transcriptomic analysis we identified the glucose-transforming polyol pathway (PP) gene aldo-keto-reductase-1-member-B1 (AKR1B1) as strongly correlated with epithelial-to-mesenchymal transition (EMT). This association was confirmed staining samples from lung cancer patients and from an EMT-driven colon cancer mouse model with p53 deletion. 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/GSE106nnn/GSE106169/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415806
Series		Accession: GSE106169	ID: 200106169

2069. Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and TWIST1 knock out U87 xenograft mice transcriptomes
(Submitter supplied) Purpose:Next-generation sequencing has revolutionized sytems-level celluar pathway analysis. The goals of this study are to compare the U87 cell xenograft GBM mice (U87 cell line) to TWIST1 knock out U87 cell xenograft GBM mice (TWIST1 knock out U87 cell line) using their transcriptomes
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106159/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415793
Series		Accession: GSE106159	ID: 200106159

2070. RNA-seq of MYC-inducible SK-MEL-28 cells
(Submitter supplied) MYC-inducible SK-MEL-28 cells with or without MYC-induction were analyzed
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/GSE101nnn/GSE101541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394756
Series		Accession: GSE101541	ID: 200101541

2071. RNA-seq of cancer cell lines treated with T-025
(Submitter supplied) 4 cancer cell lines were treated with T-025 for 6 hours T-025 is a novel small molecule inhibitor of CLK.  CLK is a kinase that regulates pre-mRNA splicing.
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/GSE101nnn/GSE101540/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394754
Series		Accession: GSE101540	ID: 200101540

2072. LEC-induced gene expression changes in melanoma cells
(Submitter supplied) RNA sequencing to analyze the gene expression changes in the WM852 and Bowes melanoma cells upon their co-culture with lymphatic endothelial cells (LECs). Platforms: NextSeq500 sequencer (Illumina) as quadruplicates
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/GSE100nnn/GSE100269/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391183
Series		Accession: GSE100269	ID: 200100269

2073. EWSR1 influences alternative splicing through direct and indirect mechanisms
(Submitter supplied) FET family RNA binding proteins are implicated in cancer and neurological disorders and yet their biological function is incompletely understood. We used cross-linking and immunoprecipitation followed by high-throughput sequencing (HITS-CLIP) as well as gene expression and alternative splicing analysis by RNAseq to characterize the molecular function of the FET family RNA binding protein EWSR1. In HeLA cells, EWSR1 binding is enriched at 3’UTRs and at both 5’ exon/intron and 3’ intron/exon boundaries. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL9115 9 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98836/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386334
Series		Accession: GSE98836	ID: 200098836

2074. Next Generation Sequencing Analysis of control and siSRSF1 treated RKO cell Transcriptomes
(Submitter supplied) We treated the RKO cells with siSRSF1 or control siRNA for 48 hours. Then we extracted the RNAs and performed the next generation sequencing. By comparing sequcing data from siSRSF1 and contron siRNA treated samples, we profiled the gene expression regulated by siRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98508/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385313
Series		Accession: GSE98508	ID: 200098508

2075. The energetics and physiological impact of cohesin extrusion
(Submitter supplied) Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo, and thus, its functional impact and energetics are unknown. Using ultra-deep Hi-C, we show that loop domains form by a process that requires cohesin ATPases. Once formed, however, loops and compartments are maintained for hours without energy input. more...
Organism:	Mus musculus; Homo sapiens
Type:		Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
6 related Platforms 352 Samples
FTP download: GEO (BED, BEDGRAPH, BW, HIC, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98119/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384026
Series		Accession: GSE98119	ID: 200098119

2076. UMI-count modeling and differential expression analysis for single-cell RNA sequencing
(Submitter supplied) Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41. We also inlcude a bulk RNA-seq study of unsorted and sorted cells using CD44 as a marker
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (MTX, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453548
Series		Accession: GSE113660	ID: 200113660

2077. Sex differences in transcriptomic profiles in aged kidney cells of renin lineage
(Submitter supplied) Renin expressing cells in the kidney’s juxta-glomeruluar compartment likely also serve as progenitors for adult glomerular cells in disease. Although these cells of renin lineage (CoRL) decrease in number with advancing kidney age, accompanied by less responsiveness to typical stimuli such as ACE-inhibition, mechanisms and the impact of sex as a biological variable with age are not known. Accordingly, labeled CoRL were sorted from individual young (2m) and aged (27m) male and female Ren1cCre|ZsGreen reporter mice, and their transcriptomic profiles analyzed by RNA seq. 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/GSE113nnn/GSE113195/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450423
Series		Accession: GSE113195	ID: 200113195

2078. Transcriptome analysis of human embryonic stem cells (hESCs) and human fibroblasts upon rapamycin
(Submitter supplied) Rapamycin inhibits mTORC1 complex in a variety of cells. We demonstrated that hESCs are more sensitive to rapamycin treatment as compared to somatic cells (BJ Fibroblasts) and also certain cancer cells (KBM7 cells). To study the molecular mechanisms of this disparity, we performed a transcriptome analysis (RNAseq) of rapamycin-treated hESCs and human fibroblasts for two time points (2 and 4 days of treatment).
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/GSE107nnn/GSE107965/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422061
Series		Accession: GSE107965	ID: 200107965

2079. RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
(Submitter supplied) G-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neurodegenerative disease and cancer. However, detailed knowledge of rG4s and their binding partners is lacking. Here, a systematic, unbiased affinity proteomics approach identified 80 potential high-confidence interactors of the rG4 structure in the 5’UTR of the NRAS oncogene. Using epitope-tagged protein expression, we validated a subset of interactions including DDX3X, DDX5, DDX17, DHX9, DHX36, FXR1, FXR2, GRSF1 and NSUN5. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (BED, BEDGRAPH, FA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417119
Series		Accession: GSE106476	ID: 200106476

2080. C/EBPα overexpression overrides epigenetic reprogramming by RUNX1-ETO and RUNX1-EVI1 [RNA-seq]
(Submitter supplied) Acute myeloid leukemia (AML) is a heterogeneous disease caused by recurrent mutations in the transcription regulatory machinery. As a result, malignant myeloid cells display abnormal growth and are blocked in differentiation. One type of recurrent mutations affects RUNX1 which is subject to mutations and translocations, the latter giving rise to fusion proteins with aberrant transcriptional activities. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102730/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398538
Series		Accession: GSE102730	ID: 200102730

2081. Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx
(Submitter supplied) In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication and acts as host gene trans-regulator. However, functionally relevant spatiotemporal localization and interactions of cccDNA and HBx remain to be understood. This is the first study utilizing circularized chromosome conformation capture (4C) to identify regional virus-host genome interactions. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL19057 31 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100400/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391572
Series		Accession: GSE100400	ID: 200100400

2082. Gene expression profiling of melanoma cell lines by RNASeq
(Submitter supplied) Panel of 53 melanoma cell lines were gene expression profiled by RNA-Seq for molecular classification
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/GSE80nnn/GSE80829/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320101
Series		Accession: GSE80829	ID: 200080829

2083. Expression and methylation profiling of esophageal NEC
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by array; Non-coding RNA profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL20157 GPL13534 GPL16791 6 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113779/
Series		Accession: GSE113779	ID: 200113779

2084. Analysis of a case of esophageal NEC at transcriptome level
(Submitter supplied) RNA-seq of a paired esophageal NEC sample and the corresponding normal esophageal sample from the same individual.
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/GSE113nnn/GSE113777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453981
Series		Accession: GSE113777	ID: 200113777

2085. DAOY-Notch1/Notch2 knockout: transcriptome comparison
(Submitter supplied) Hyperactivation of Notch signaling and the cellular hypoxic response are frequently observed in cancers, with increasing reports of connections to tumor initiation and progression. The two signaling mechanisms are known to intersect, but while it is well established that hypoxia regulates Notch signaling, less is known about whether Notch can regulate the cellular hypoxic response. We now report that Notch signaling specifically controls expression of HIF2a, a key mediator of the cellular hypoxic response. 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/GSE113nnn/GSE113753/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453919
Series		Accession: GSE113753	ID: 200113753

2086. NUPR1 depletion activates premature senescence and overcomes tamoxifen resistance in breast cancer cells
(Submitter supplied) Background Selective estrogen receptor modulators such as tamoxifen (Tam) and its derivatives are anti-breast cancer drugs known to cause resistance during chemotherapy. To support cellular homeostasis and mitigate chemotherapeutic stress, cancer cells may gain a series of adaptive intracellular processes including autophagy for survival. Methods We utilized patient breast tumor tissue microarrays, human breast cancer cell lines, xenograft mouse model to investigate autophagic flux changes by NUPR1-mediated transcriptional control. 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/GSE104nnn/GSE104050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA408094
Series		Accession: GSE104050	ID: 200104050

2087. MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing
(Submitter supplied) Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks.  However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development.  Here we utilized TALENs to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL23227 GPL15520 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103811/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407088
Series		Accession: GSE103811	ID: 200103811

2088. Effect of NORAD shRNA on A549 cells treated with TGF-beta
(Submitter supplied) We evaluated the effect of NORAD (also known as LINC00657 or LOC647979) shRNA on TGF-beta induced changes in the gene expression in A549 cells by RNA-seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430367
Series		Accession: GSE109296	ID: 200109296

2089. The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 Acute Myelogenous Leukemia
(Submitter supplied) Acute Myeloid Leukemia (AML) with MLL gene rearrangements demonstrate unique gene expression profiles driven by MLL-fusion proteins. Here, we identify the circadian clock transcription factor SHARP1 as a novel oncogenic target in MLL-AF6 AML, which has the worst prognosis among all subtypes of MLL rearranged AMLs. SHARP1 is expressed solely in MLL-AF6 AML, and its expression is regulated directly by MLL-AF6 / DOT1L. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 23 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377303
Series		Accession: GSE95511	ID: 200095511

2090. RNA sequencing analysis of adult mixed phenotype acute leukemia (MPAL)
(Submitter supplied) RNA sequencing analysis was performed from bone marrow samples of 24 adult mixed phenotype acute leukemia (MPAL) patients
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/GSE113nnn/GSE113601/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA453199
Series		Accession: GSE113601	ID: 200113601

2091. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 21 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111211/
Series		Accession: GSE111211	ID: 200111211

2092. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression [ELL2 rescue]
(Submitter supplied) To understand the biological mechanism of ELL2 in multiple myeloma (MM), we show that the MM risk allele lowers ELL2 expression in CD138+ plasma cells (Pcombined=2.5×10-27; bcombined=-0.24 s.d.), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. more...
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/GSE111nnn/GSE111210/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436170
Series		Accession: GSE111210	ID: 200111210

2093. The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression [ELL2 KO]
(Submitter supplied) To understand the biological mechanism of ELL2 in multiple myeloma (MM), we show that the MM risk allele lowers ELL2 expression in CD138+ plasma cells (Pcombined=2.5×10-27; bcombined=-0.24 s.d.), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. 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/GSE111nnn/GSE111199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436147
Series		Accession: GSE111199	ID: 200111199

2094. Molecular signature of human cerebral organoids glioma model
(Submitter supplied) We have developed a cancer model of gliomas in human cerebral organoids by CRISPR/Cas9 technology to target a Harvey-Ras (H-RAS) G12V-IRES-tdTomato construct by homologous recombination into the TP53 locus. 16 weeks after electrporation, these tdTomato positive transduced cells were sorted and compared to nontransduced cellls by RNA-seq and gene expression profiles were compared to each other and with human glioma Verhaak subtype signatures.
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/GSE109nnn/GSE109982/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432513
Series		Accession: GSE109982	ID: 200109982

2095. Human T-cell lymphoblastic lymphoma samples and control thymuses
(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: GPL10999 GPL11154 20 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109234/
Series		Accession: GSE109234	ID: 200109234

2096. RNA-Seq in human T-cell lymphoblastic lymphoma samples and control thymuses
(Submitter supplied) Precursor T-cell lymphoblastic neoplasms are aggressive haematological neoplasm that most often manifest with extensive marrow and blood affectation (T-cell acute lymphoblastic leukaemia or T-ALL) or less commonly as a thymic mass with limited bone marrow infiltration (T-cell lymphoblastic lymphoma or T-LBL). Here we show data from RNA-Seq in a sample series of T-LBL from Spanish patients.The goal was to determine the levels of expression of coding genes and microRNAs, and to identify all genetic variants including SNVs, indels, and fusion transcripts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109231/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430225
Series		Accession: GSE109231	ID: 200109231

2097. RNA editing in nascent RNA affects pre-mRNA splicing
(Submitter supplied) In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress in understanding their global RNA targets and regulatory pathways. 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/GSE105nnn/GSE105773/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415378
Series		Accession: GSE105773	ID: 200105773

2098. RNA-Seq analysis of prostate cancer cell line C4-2 treated with siRNA control (siCont), siEAF2, sip53 or concurrent siEAF2 and sip53
(Submitter supplied) The tumor suppressor genes EAF2 and p53 are frequently dysregulated in prostate cancers. Recently, we reported that concurrent p53 nuclear staining and EAF2 downregulation were associated with high Gleason score. Combined loss of EAF2 and p53 in a murine model induced prostate tumors, and concurrent knockdown of EAF2 and p53 in prostate cancer cells enhanced proliferation and migration, further suggesting that EAF2 and p53 could functionally interact in the suppression of prostate tumorigenesis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413694
Series		Accession: GSE104729	ID: 200104729

2099. Effect of low-dose sorafenib and alkylating agents in inflammation and angiogenesis in breast cancer
(Submitter supplied) Molecular targeted compounds are emerging as important component to improve the efficacy of classical chemotherapeutics. In this study, we tested whether using low dose sorafenib to reduce off target inhibitions of kinases impacts the antitumor effect of alkylating agents in breast cancer models.
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/GSE99536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388753
Series		Accession: GSE99536	ID: 200099536

2100. Alternative splicing regulated by QKI and RBFOX1 promotes the mesenchymal cell state 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: GPL18573 19 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98210/
Series		Accession: GSE98210	ID: 200098210

2101. eCLIP in immortalized human mammary epithelial cells
(Submitter supplied) The epithelial-to-mesenchymal transition (EMT) contributes to tumor heterogeneity and has been implicated in tumor initiation and metastasis. To systematically identify genes involved in EMT, we performed a genome-scale expression screen in human mammary epithelial cells and found a striking enrichment in RNA splicing factors. In particular, the RNA-binding proteins QKI and RBFOX1 were necessary and sufficient to promote EMT and stem-like states. 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/GSE98nnn/GSE98209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384254
Series		Accession: GSE98209	ID: 200098209

2102. RNA-sequencing in immortalized human mammary epithelial cells
(Submitter supplied) The epithelial-to-mesenchymal transition (EMT) contributes to tumor heterogeneity and has been implicated in tumor initiation and metastasis. To systematically identify genes involved in EMT, we performed a genome-scale expression screen in human mammary epithelial cells and found a striking enrichment in RNA splicing factors. In particular, the RNA-binding proteins QKI and RBFOX1 were necessary and sufficient to promote EMT and stem-like states. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 13 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98208/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384255
Series		Accession: GSE98208	ID: 200098208

2103. Functional co-operativity of long-noncoding RNAs at the neuroblastoma susceptibility locus 6p22.3 controls disease progression via USP36-CHD7-SOX9 gene regulatory axis.
(Submitter supplied) We report 6p22 locus lncRNAs, which were identified as differentially expressed between high and non-high risk neuroblastoma  tumors using RNA sequencing. we identified CASC15-003 and CASC15-004 lncRNAs act as prognostic biomarker in neuroblastoma.
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/GSE100nnn/GSE100215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391009
Series		Accession: GSE100215	ID: 200100215

2104. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance (RNA-Seq)
(Submitter supplied) BACKGROUND: Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. more...
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/GSE98nnn/GSE98812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386287
Series		Accession: GSE98812	ID: 200098812

2105. Expression Profiling of Cisplatin Resistant SKOV3 Cell Lines vs. Wild Type SKOV3 Cell Lines
(Submitter supplied) Ovarian cancer SKOV3 cells were studied to profile the expression of wild type (WT, Cisplatin Susceptible) cells and Cisplatin Resistant (CR) cells. The goal was to gain insights or to build hypotheses into the mechanisms of Cisplatin resistance in this cell-based model.
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/GSE98nnn/GSE98559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385512
Series		Accession: GSE98559	ID: 200098559

2106. Long ncRNA Landscape in the Ileum of Treatment Naïve Early Onset Crohn Disease
(Submitter supplied) Objective: Long non-coding RNAs (lncRNA) regulate gene transcription and diverse cellular functions. We previously defined a novel core inflammatory and metabolic ileal gene signature in treatment naïve pediatric Crohn Disease (CD), however, genome-wide characterization of lncRNA expression was lacking. We now extend our analyses to define a more comprehensive view that includes lncRNA. Design: Using RNAseq, we performed a systematic profiling of lncRNAs and protein-coding genes expression in 177 ileal biopsies. 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/GSE94nnn/GSE94578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371496
Series		Accession: GSE94578	ID: 200094578

2107. Clinker: visualizing fusion genes detected in RNA-seq data
(Submitter supplied) Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important therapeutic targets. While there are many ways to identify fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes. 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/GSE113nnn/GSE113504/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451407
Series		Accession: GSE113504	ID: 200113504

2108. RNAseq Study in CC-671 Treated Cal-51 Cells
(Submitter supplied) CC-671 has been identified as an inhibitor of Cdc2-like kinase 2 (CLK2) and TTK in direct enzyme assays. CLK2 is a member of the CLK family that phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex as part of a regulatory mechanism for control of pre-mRNA splicing.  SR proteins are a family of small nuclear ribonucleoprotein particle (snRNP) splicing factors involved in constitutive and alternative splicing. 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/GSE113nnn/GSE113426/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451158
Series		Accession: GSE113426	ID: 200113426

2109. Transcriptome analysis of immortalized and transformed human IMR90 fibroblasts
(Submitter supplied) RNA polymerase (Pol) III transcribes small untranslated RNAs that are essential for cellular homeostasis and growth. Its activity is regulated by inactivation of tumor suppressor proteins and overexpression of the oncogene c-MYC, but the concerted action of these tumor-promoting factors on Pol III transcription has not yet been assessed. In order to comprehensively analyse the regulation of Pol III transcription during tumorigenesis we employ a model system that relies on the expression of five genetic elements to achieve cellular transformation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99212/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381003
Series		Accession: GSE99212	ID: 200099212

2110. The role of AR associated protein and lncRNA in androgen signaling
(Submitter supplied) Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed RNA sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Long term androgen deprivation (LTAD) to explore the differences of androgen signaling in prostate cancer progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL13393 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94028/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363077
Series		Accession: GSE94028	ID: 200094028

2111. Gene expression profiling study by RNA-seq for identifying gene signatures associated with castration-refractory prostate cancer (CRPC) development.
(Submitter supplied) The objective of this study is to identify gene signature associated with castration-refractory prostate cancer (CRPC) development. We carried out RNA-seq based transcriptome profiling using 45 prostate samples with various disease progression steps such as benign prostate hyperplasia (BPH), primary cancer of prostate (CaP), advanced CaP and CRPC. Via various statistical analyses, we identified significant gene set associated with each progression step and observed that AR was the only gene feature associated with all progression steps, indicating that AR is the crucial mediator of and has a diverse activity across the CaP progressions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 45 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80609/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319483
Series		Accession: GSE80609	ID: 200080609

2112. RNA Sequencing of adult high grade glioblastoma tumors
(Submitter supplied) RNA extracted from fresh frozen adult high grade glioblastomas were sequenced for transcriptomic analysis.
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/GSE113nnn/GSE113474/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA451200
Series		Accession: GSE113474	ID: 200113474

2113. Single cell RNA-seq analysis of K27M-mutant glioma
(Submitter supplied) To understand the diversity of expression states within K27M-mutant gliomas, we profiled 4058 single cells, primarily from 6 K27M-mutant gliomas, by single cell RNA-seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4058 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102130/
Series		Accession: GSE102130	ID: 200102130

2114. Gene expression analysis of human CD8+ T cells treated with a DOT1L inhibitor
(Submitter supplied) Adoptive T cell therapy (ACT) is a promising therapeutic approach for cancer patients.  The use of allogeneic T cell grafts will improve its applicability and versatility provided that inherent allogeneic responses are controlled.  Through extensive chemical probe screening, we found that inhibiting DOT1L, a histone H3-lysine 79 methyltransferase, alleviated allogeneic T cell responses.  DOT1L inhibition with SGC0946 selectively ameliorated low-avidity T cell responses but not high-avidity antitumor T cell responses mediated by the high-affinity T cell receptor or chimeric antigen receptor. 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/GSE108nnn/GSE108694/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428310
Series		Accession: GSE108694	ID: 200108694

2115. DAOY-NERT2 Notch/Hypoxia Transcriptome Analysis
(Submitter supplied) Hyperactivation of Notch signaling and the cellular hypoxic response are frequently observed in cancers, with increasing reports of connections to tumor initiation and progression. The two signaling mechanisms are known to intersect, but while it is well established that hypoxia regulates Notch signaling, less is known about whether Notch can regulate the cellular hypoxic response. We now report that Notch signaling specifically controls expression of HIF2a, a key mediator of the cellular hypoxic response. 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/GSE113nnn/GSE113353/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450861
Series		Accession: GSE113353	ID: 200113353

2116. Iron response of HepG2 cells
(Submitter supplied) RNA-seq of HepG2 cells in response to iron
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99697/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389312
Series		Accession: GSE99697	ID: 200099697

2117. RNA-sequencing (RNA-seq) in BxPC-3 and S2-007 cell lines
(Submitter supplied) RNA sequencing technology has been carried out in order to compare mRNA expression changes in epithelial BxPC-3 versus mesenchymal S2-007 cells.
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/GSE113nnn/GSE113259/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450600
Series		Accession: GSE113259	ID: 200113259

2118. Sauchinone controls hepatic cholesterol homeostasis by the negative regulation of PCSK9 transcriptional network
(Submitter supplied) We performed transcript profiling of sauchinone treated with various doses on HepG2 cells using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.
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/GSE113247/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450545
Series		Accession: GSE113247	ID: 200113247

2119. Epigenetic changes induced by Bacteroides fragilis toxin (BFT)
(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 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113220/
Series		Accession: GSE113220	ID: 200113220

2120. Epigenetic changes induced by Bacteroides fragilis toxin (BFT) [RNA-seq]
(Submitter supplied) Purpose: The goal of this study is to determine how BFT2 alters chromatin accessibility at relatively early time points in colon epithelial cells, and to correlate the changes in chromatin accessibility with changes in gene expression, transcription factor binding sites, and the location of common single nucleotide variants (SNVs) and differentially methylated regions (DMRs) in colorectal cancer. Methods: HT29/C1 cells were plated at low density and allowed to grow for 4 days at 37C and 10% CO2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113218/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450654
Series		Accession: GSE113218	ID: 200113218

2121. An acquired vulnerability of drug resistant melanoma with therapeutic potential
(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 high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111141/
Series		Accession: GSE111141	ID: 200111141

2122. RNA Seq data: A375, A375R, A375DR vorinostat treated, and biopy samples from patients pre- and post- treated with Vorinostat
(Submitter supplied) BRAF(V600E) mutant melanomas treated with inhibitors of the BRAF and MEK kinases almost invariably develop resistance, which is frequently caused by reactivation of the Mitogen Activated Protein Kinase (MAPK) pathway. To identify novel treatment options for such patients, we searched for acquired vulnerabilities of MAPK inhibitor-resistant melanomas. We find that resistance to BRAF+MEK inhibitors is associated with increased levels of reactive oxygen species (ROS). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110948/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435114
Series		Accession: GSE110948	ID: 200110948

2123. Angiogenin/ribonuclease 5 is an EGFR ligand and a serum biomarker for erlotinib sensitivity in pancreatic cancer
(Submitter supplied) Pancreatic ribonuclease (RNase) is a secreted enzyme critical for host defense. We discover an intrinsic RNase function, serving as a ligand for epidermal growth factor receptor (EGFR), a member of receptor tyrosine kinase (RTK), in pancreatic ductal adenocarcinoma (PDAC). The closely related bovine RNase A and human RNase 5 (angiogenin/ANG) can trigger oncogenic transformation independently of their catalytic activities via direct association with EGFR. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109427/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432337
Series		Accession: GSE109427	ID: 200109427

2124. Differentially Expressed Genes upon Knockdown of ZRANB1 or EZH2 in LM2 Cells
(Submitter supplied) EZH2, the catalytic component of the Polycomb repressive complex 2 (PRC2), silences gene transcription by methylating histone H3 at lysine 27. Recently we identified ZRANB1 as the EZH2 deubiquitinase. ZRANB1 binds, deubiquitinates, and stabilizes EZH2. To determine whether ZRANB1 is a functional regulator of EZH2, we performed RNA-Seq analysis to compare the effect of ZRANB1 knockdown or EZH2 knockdown on global gene expression.
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/GSE104910/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414117
Series		Accession: GSE104910	ID: 200104910

2125. Differential Gene Expression and Pathway Analysis in Juvenile Nasopharyngeal Angiofibroma Using RNA-Sequencing
(Submitter supplied) We have identified a set of differentially expressed genes in the juvenile nasopharyngeal angiofibroma transcriptome and predict activation of the vascular endothelial growth factor and interleukin-6 signaling pathways, which represent potential molecular targets for therapy in patients with inoperable or persistent disease. These results implicate the role of fibroblasts as a tumor cell type driving disease progression.
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/GSE99nnn/GSE99247/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387701
Series		Accession: GSE99247	ID: 200099247

2126. Treatment of SW480 colon cancer cell induced xenografts with AZD and DBZ
(Submitter supplied) RNASeq data from replicates with and without treatment of SW480 colon cancer cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98922/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386891
Series		Accession: GSE98922	ID: 200098922

2127. TGF-β regulation of miRNA expression in pancreatic cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16142 39 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88759/
Series		Accession: GSE88759	ID: 200088759

2128. Identification of miR-100 and miR-125b targets by AGO2 RIP-seq and RNA-seq after ectopic expression of miR-100 or miR-125b and evaluation of the TGFb expression signature in PANC-1 cells by RNA-seq
(Submitter supplied) To identify targets post-transcriptionally regulated by miR-100 and miR-125b, we have performed AGO2 RIP-seq and RNA-seq following overexpression of the two miRNAs in PANC-1 cells.  In addition, we have carried out RNA-seq following TGFb stimulus to evaluate changes in gene expression driven by TGFb.
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/GSE88nnn/GSE88757/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348471
Series		Accession: GSE88757	ID: 200088757

2129. Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_3]
(Submitter supplied) Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 325 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113198/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450412
Series		Accession: GSE113198	ID: 200113198

2130. Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [Individual 4..7]
(Submitter supplied) Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. 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/GSE113nnn/GSE113196/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450410
Series		Accession: GSE113196	ID: 200113196

2131. Multi-omics Profiling of Younger Asian Breast Cancers Reveals Distinctive Molecular Signatures
(Submitter supplied) We observed higher proportions of HER2+ and Luminal B but lower proportions of ER+ and Luminal A subtypes along with lower estrogen receptor (ER) expression in SMC compared to TCGA. Germline pathogenic mutations affecting BRCA1 or BRCA2 were found in 11% of SMC but only 5% of TCGA. TP53 was also more frequently mutated in SMC (48%) than in TCGA (32%).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL24896 178 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113184/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450393
Series		Accession: GSE113184	ID: 200113184

2132. Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_2]
(Submitter supplied) Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 246 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450371
Series		Accession: GSE113127	ID: 200113127

2133. Single Cell RNA sequencing of Adult Human Breast Epithelial Cells [C1_Individual_1]
(Submitter supplied) Breast cancer arises from breast epithelial cells that acquire genetic alterations leading to subsequent loss of tissue homeostasis. Several distinct epithelial subpopulations have been proposed, but complete understanding of the spectrum of heterogeneity and differentiation hierarchy in the human breast remains elusive. Here, we used single-cell mRNA sequencing (scRNAseq) to profile the transcriptomes of 25,790 primary human breast epithelial cells isolated from reduction mammoplasties of seven individuals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 296 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113099/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450372
Series		Accession: GSE113099	ID: 200113099

2134. Tracking transcriptional changes in a species-specific manner during experimental hepatoblastoma progression in vivo
(Submitter supplied) Hepatoblastoma is a primitive liver cancer occurring mainly in infants with defined molecular alterations driving its progression, which is difficult to model in vivo. Here we present a new animal model for hepatoblastoma on the chick chorioallantoic membrane (CAM), which recapitulates relevant features of hepatoblastoma in patients. Expression of classic tumor-associated proteins such as β-catenin, EpCAM and CK19 was maintained in acini-like organized tumors on CAM, as was synthesis of AFP, a tumor marker used for monitoring patient response. more...
Organism:	Gallus gallus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16133 GPL11154 GPL16791 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101413/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394137
Series		Accession: GSE101413	ID: 200101413

2135. A Nucleosome Destabilizing Factor that Facilitates Transcription in Chromatin
(Submitter supplied) Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. more...
Organism:	Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL21103 GPL20301 28 Samples
FTP download: GEO (BED, BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109690/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431727
Series		Accession: GSE109690	ID: 200109690

2136. Alternate assembly of SDHA connects energy stress to metabolic checkpoint and DNA synthesis
(Submitter supplied) Cell growth and survival depend on a delicate balance between energy production and synthesis of metabolites. We have discovered that an alternative mitochondrial complex II (CII) assembly, designated here as CIIlow, serves as a check-point for metabolite biosynthesis under bioenergetic stress, with cells suppressing their energy utilization by modulating DNA synthesis and cell cycle progression. Depletion of CIIlow leads to an imbalance in energy utilization and metabolite synthesis, as evidenced by recovery of the de novo pyrimidine pathway and unlocking cell cycle arrest from the S-phase. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108938/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429204
Series		Accession: GSE108938	ID: 200108938

2137. Immune Profiling of Premalignant Lesions in Patients with Lynch Syndrome 
(Submitter supplied) mRNA expression from adenomas of patients with Lynch Syndrome and Familial Adenomatous Polyposis
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/GSE106nnn/GSE106500/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417076
Series		Accession: GSE106500	ID: 200106500

2138. bigSCale: An Analytical Framework for Big-Scale Single Cell Data
(Submitter supplied) Single-cell RNA sequencing significantly deepened our insights into complex tissues and latest techniques are capable to analyze ten-thousands of cells simultaneously. With bigSCale, we provide an analytical framework being scalable to analyze millions of cells, addressing challenges of future large data sets. Unlike other methods, bigSCale does not constrain data to fit an a priori-defined distribution and instead uses an accurate numerical model of noise. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1847 Samples
FTP download: GEO (CSV, H5, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102934/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399496
Series		Accession: GSE102934	ID: 200102934

2139. Transcriptional effect of ETV1 knockdown in melanoma cells
(Submitter supplied) ETV1 is amplified in a subset of melanomas. Here, we performed RNA-seq on two BRAF V600E mutant melonoma cell lines transduced with a scrambed shRNA and two individual ETV1 shRNA
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/GSE80nnn/GSE80352/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319396
Series		Accession: GSE80352	ID: 200080352

2140. Role of COP1 on MAP kinase transcriptional output in melanoma
(Submitter supplied) COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of COP1 in the regulation of MAP kianse transciptional output.  We generated A375 melanoma cells with CRISPR/Cas9 mediated COP1 (gene symbol RFWD) knockout. We treated control sgEGFP and COP1 loss sgCOP1 cells with vehicle, 1 µM vemurafinib, or 5 nM trametinib for 8 hours and isolated RNA for sequencing.
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/GSE80nnn/GSE80313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318531
Series		Accession: GSE80313	ID: 200080313

2141. Role of COP1 on MAP kinase transcriptional output in gastrointestinal stromal tumor
(Submitter supplied) COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of COP1 in the regulation of MAP kianse transciptional output.  We transfected GIST882 cells with siRNA against a scrambled sequence and two sequences against COP1. We treated cells for 8 hours with vehicle or 100 nM PD0325901 in duplicate and isolated RNA for sequencing.
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/GSE80nnn/GSE80305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318528
Series		Accession: GSE80305	ID: 200080305

2142. Critical role for Lymphocytes in Producing FLT3LG in Tumors and Driving Checkpoint Therapy-Receptive Immune Microenvironments
(Submitter supplied) Intratumoral stimulatory dendritic cells (SDCs) play an important role in locally restimulating cytotoxic T cells and driving immune responses against cancer. However, the mechanisms that control SDC numbers remain poorly understood. In human melanoma, SDC numbers correlated with intratumoral expression of the gene encoding the cytokine FLT3LG, and we subsequently found in mouse and human tumors that this cytokine was predominantly produced by lymphocytes, notably including natural killer (NK) cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE113nnn/GSE113126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA450084
Series		Accession: GSE113126	ID: 200113126

2143. Role of Epstein-Barr Virus (EBV) latency protein EBNA3C in EBV-induced lymphomagenesis in a cord blood-humanized mouse model
(Submitter supplied) This study compares cellular and viral gene expression in a cord blood-humanized (CBH) mouse model infected with wild-type Epstein-Barr virus (WT), versus a mutant EBV deleted in the latent viral EBNA3C gene (∆3C). EBV causes human B-cell lymphomas and transforms B cells in vitro. EBNA3C, an EBV protein expressed in latently infected cells, is required for EBV transformation of B cells in vitro. However, many EBV+ lymphomas in humans do not express this protein, suggesting that it may be less important in vivo or that cellular mutations and/or signaling pathways may obviate the need for EBNA3C. more...
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/GSE113nnn/GSE113070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449926
Series		Accession: GSE113070	ID: 200113070

2144. Seletive inhibition of CDK9 in DLBCL cell lines
(Submitter supplied) Deregulation of the MYC transcription factor is a key driver in lymphomagenesis. MYC induces global changes in gene expression that contribute to cell growth, proliferation and oncogenesis by stimulating the activity of RNA polymerases. A key feature in its ability to stimulate RNA Pol II activity is recruitment of pTEFb, an elongation factor whose catalytic core comprises CDK9/cyclin T complexes. Hence, MYC expression and function may be susceptible to CDK9 inhibition. more...
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/GSE113nnn/GSE113035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA449845
Series		Accession: GSE113035	ID: 200113035

2145. Temporal RNA-seq analysis of human skeletal myotubes synchronized in vitro
(Submitter supplied) The circadian regulation of transcriptional processes has a broad impact on cell metabolism. Here, we compared the diurnal transcriptome of human skeletal muscle conducted on serial muscle biopsies in vivo with profiles of human skeletal myotubes synchronized in vitro. Extensive rhythmic transcription was observed in human skeletal muscle in comparison to in vitro cell culture. However, nearly half of the in vivo rhythmicity was lost at the mRNA accumulation level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 100 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109825/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432088
Series		Accession: GSE109825	ID: 200109825

2146. Differential effects of estrogen receptor beta isoforms on glioblastoma progression
(Submitter supplied) We examined the transcriptional changes modulated by knocking out ERβ and reintroduction of ERβ1 and ERβ5 isoforms by perfroming global transcriptome analysis. ERβ was knocked out in U87 cells using CRISPR/Cas9 system and reintroduced the ERβ1 and ERβ5 isoforms in knockout background. RNA was isolated from control U87, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells and utilized for RNA-seq analysis. Our results demonstrated that ERβ-KO, ERβ1 and ERβ5 modulated unique pathways  including NF-κB singaling, Jak/STAT pathway and mTOR signaling.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412261
Series		Accession: GSE104296	ID: 200104296

2147. RNA sequencing (RNA-SEQ) of PSPC1 Knockout in A549 cells with TGFb1 stimulation
(Submitter supplied) We show that PSPC1 is required for cancer cell motilities and stemness properties in vitro and lung metastasis in vivo. We used high throughput sequencing to analyze the PSPC1 regulated gene expression. Loss of PSPC1 results in significant gene expression level changes in thousands of individual transcripts in key regulators of the EMT, CSCs and TGFb signaling.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103293/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401901
Series		Accession: GSE103293	ID: 200103293

2148. Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency
(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; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL13534 GPL10999 212 Samples
FTP download: GEO (BW, IDAT, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90015/
Series		Accession: GSE90015	ID: 200090015

2149. Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [RNA-seq analysis]
(Submitter supplied) Human induced Pluripotent Stem cells (iPSCs) can be generated by enforced-expression of OCT3/4, SOX2, KLF4 and c-MYC (OSKM) via intermediate state that is labeled with a surface antigen TRA-1-60.  However the event during conversion of somatic cells to TRA-1-60 positive (+) fate by OSKM is still unclear. Here we show that TRA-1-60 (+) cells emerged from ESRG (+) cells with proliferation independent manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89975/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354485
Series		Accession: GSE89975	ID: 200089975

2150. Distinct Transcriptomic and Exomic Abnormalities within Myelodysplastic Syndrome Marrow Cells
(Submitter supplied) Prior studies using DNA microarray platforms have shown alterations of gene expression profiles (GEPs) of marrow cells in myelodysplastic syndromes (MDS). Using the increased sensitivity and accuracy of high-throughput RNA sequencing (RNA-Seq) for detecting and quantifying mRNA transcripts, our study has demonstrated novel significant differences in GEPs between MDS and normal CD34+ marrow cells with 41 genes identified as disease classifiers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 67 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111085/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435879
Series		Accession: GSE111085	ID: 200111085

2151. Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO (VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110538/
Series		Accession: GSE110538	ID: 200110538

2152. Active BRAF-V600E is the key player in generation of a sessile serrated polyp-specific DNA methylation profile (RNA-seq data set)
(Submitter supplied) Screening and surveillance of colorectal cancers (CRCs) using advanced colonoscopy technologies have significantly reduced the incidence and mortality rates of CRCs in recent years. However, a significant portion of CRCs are still remained undiagnosed, especially those involving sessile serrated adenomas/polyps (SSA/P), most likely due to their flat shape and the excessive amounts of secreted mucin that cover the polyps, making them invisible for colonoscopy. 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/GSE110nnn/GSE110536/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433955
Series		Accession: GSE110536	ID: 200110536

2153. Tumor evolution and drug response in patient-derived organoid models of bladder cancer
(Submitter supplied) Bladder cancer is the fifth most prevalent cancer in the U.S., yet is understudied and relatively lacking in suitable models. Here we describe a biobank of patient-derived organoid lines that recapitulates the spectrum of human bladder cancer at the histopathological and molecular levels. Organoid lines can be established efficiently from patient biopsies, including from patients before and after disease recurrence, and are interconvertible with orthotopic xenografts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103990/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407895
Series		Accession: GSE103990	ID: 200103990

2154. Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [Polysome-Seq]
(Submitter supplied) Pseudouridylation (pseudouridine) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of pseudouridine remains poorly understood. Here, we show that a pseudouridine-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the pseudouridine ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. 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/GSE101nnn/GSE101485/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394611
Series		Accession: GSE101485	ID: 200101485

2155. 4C-seq of insulin promoter, knockdown of INS promoter activity and Genome-wide maps of chromatin state in EndoC-βH1 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; Other
Platform: GPL16791 18 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112346/
Series		Accession: GSE112346	ID: 200112346

2156. Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
(Submitter supplied) Background: Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 63 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378953
Series		Accession: GSE96538	ID: 200096538

2157. Time-course RNA-sequencing of human induced regulatory T cell (iTreg) differentiation
(Submitter supplied) Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first- in-man trials of Treg transfer achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 81 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94396/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369563
Series		Accession: GSE94396	ID: 200094396

2158. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis [Quant-Seq]
(Submitter supplied) Defining direct targets of transcription factors and regulatory pathways is key to understanding their role in physiology and disease. Here we combine SLAM-seq, a novel method for direct quantification of newly synthesized mRNAs, with pharmacological and rapid chemical-genetic perturbation to interrogate primary transcriptional targets of BRD4 and MYC and define the response to BET bromodomain inhibitors (BETi). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 19 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111457/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437106
Series		Accession: GSE111457	ID: 200111457

2159. Acquired resistance to MEK-CDK4/6 inhibitor combinations in cutaneous melanoma
(Submitter supplied) Continuous MEK and CDK4/6 inhibition is effective in pre-clinical models, nevertheless, some tumors acquire resistance that was associated with enhanced phospho S6. To characterize the mechanism mediating the upregulation of mTOR-S6 pathway in these tumors, we performed RNA sequencing and targeted panel sequencing on xenograft tumors that progressed on either MEK plus CDK4/6 inhibitors (ComboR) or control diet. 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/GSE111nnn/GSE111005/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435576
Series		Accession: GSE111005	ID: 200111005

2160. RNA sequencing to study transcriptomic changes in DLD-1 (colorectal adenocarcinoma) cells exposed to soft polyacrylamide matrices (~2 kPa and ~55 kPa) for short time scale of 90 minutes
(Submitter supplied) Aim: To examine transcriptional changes in DLD-1 cells exposed to softer matrices (2 kPa and 55 kPa) and identify the chromosomes that are enriched with maximmally deregulated genes Methods: DLD-1 cells (otherwise growing on stiff tissue culture plastic substrates) were exposed to softer matrices for 90 minutes and to collagen coated glass coverslips (served as control) served as control) Results: RNA sequencing revealed nearly equivalent transcriptional deregulation in cells on both the polyacrylamide matrices (783 genes up and 872 genes down on 2 kPa, 649 genes up and 783 genes down on 55 kPa) when compared to cells on glass. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (FA, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108907/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429111
Series		Accession: GSE108907	ID: 200108907

2161. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis [SLAM-seq]
(Submitter supplied) Defining direct targets of transcription factors and regulatory pathways is key to understanding their role in physiology and disease. Here we combine SLAM-seq, a novel method for direct quantification of newly synthesized mRNAs, with pharmacological and rapid chemical-genetic perturbation to interrogate primary transcriptional targets of BRD4 and MYC and define the response to BET bromodomain inhibitors (BETi). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18460 GPL16791 104 Samples
FTP download: GEO (BED, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393189
Series		Accession: GSE100708	ID: 200100708

2162. A20 regulates canonical wnt-signaling through an interaction with RIPK4
(Submitter supplied) The role of A20 in regulating canonical wnt signaling was investigated in colon cancer cell lines (RKO) by RNAseq
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/GSE111nnn/GSE111084/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435878
Series		Accession: GSE111084	ID: 200111084

2163. MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia.
(Submitter supplied) The clinical efficacy displayed by ibrutinib in chronic lymphocytic leukemia (CLL) has been challenged by the frequent emergence of resistant clones. The ibrutinib target, Bruton's tyrosine kinase (BTK), is essential for B-cell receptor signaling, and most resistant cases carry mutations in BTK or PLCG2, a downstream effector target of BTK. Recent findings show that MI-2, a small molecule inhibitor of the para-caspase MALT1, is effective in preclinical models of another type of BCR pathway-dependent lymphoma. 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/GSE98nnn/GSE98206/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384250
Series		Accession: GSE98206	ID: 200098206

2164. Development and Verification of an RNA-Seq Assay for the Detection of Gene Fusions in Tumors
(Submitter supplied) Purpose: Assessment of the performance characteristics of an RNA-Seq assay designed to detect gene fusions in 573 genes to aid in the management of cancer patients. Methods: Polyadenylated RNA was converted to cDNA which was then used to prepare NGS libraries that were sequenced on a HiSeq 2500 instrument and analyzed with an in-house developed bioinformatic pipeline. Results: The assay identified 38 of 41 (93%) gene fusions previously detected by a different laboratory using FISH, RT-PCR, or RNA-Seq for a sensitivity of 93%. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 54 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111320/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436593
Series		Accession: GSE111320	ID: 200111320

2165. RNA seq_PDX2_SHP099
(Submitter supplied) RNA seq data of PDX2 treated with vehicle of SHP099 --> to check senescence and SASP gene expression signatures
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/GSE109nnn/GSE109270/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430265
Series		Accession: GSE109270	ID: 200109270

2166. Global transcriptional changes in U87MG glioblastoma cells upon shRNA-mediated TRIM52 knockdown
(Submitter supplied) shRNA-mediated ablation of the RING-finger protein TRIM52 from multiple glioblastoma cell lines reduces proliferation and tumorigenesis. To identify gene signatures underlying this phenomenon, transcritional profile of TRIM52 knockdown cells was compared to control cells. Upon TRIM52 ablation, we find 278 differentially regulated genes. Gene ontology analysis reveals that many of the upregulated genes are associated with glycolysis and biosynthetic processes.
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/GSE107nnn/GSE107932/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421947
Series		Accession: GSE107932	ID: 200107932

2167. Epigenetic Reprogramming of mutant RAS-driven Rhabdomyosarcoma via MEK Inhibition
(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; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL1261 GPL18573 GPL11154 60 Samples
FTP download: GEO (BED, CEL, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85171/
Series		Accession: GSE85171	ID: 200085171

2168. MEK inhibition rewires enhancer landscapes in RAS-driven Rhabdomyosarcoma to unlock a myogenic differentation block
(Submitter supplied) Trametinib-treated rhabdomyosarcoma cells undergo transcriptional reprogramming akin to myogenic differentiation.   This reprogramming is induced by loss of ERK-mediated inhibition of MYOG expression.  Restoration of MYOG allows establishment of super-enhancers at genes expressed by terminally differentiated myotubes.  Our findings demonstrate that aberrant MAP kinase activity blocks differentiation in rhabdomyosarcoma and highlight trametinib as a potential therapeutic for RAS-mutated rhabdomyosarcoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85170/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336381
Series		Accession: GSE85170	ID: 200085170

2169. Effect of human pulmonary MSCs isolated from normal and tumor tissues on the expression profile of primary lung cancer cells
(Submitter supplied) Metastasis is a multi-step process that involves direct cross-talk between cancer cells and their microenvironment. Here we assessed the effect of paired mesenchymal stem cells (MSCs) isolated from the tumor tissue (T-) and normal lung adjacent tissue (N-) on the expression profile of primary lung cancer cells. We observed that MSCs induce the expression of genes in tumor cells associated with an aggressive phenotype and promote early tumor cell dissemination. 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/GSE104858/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413364
Series		Accession: GSE104858	ID: 200104858

2170. PARN and TOE1 constitute a 3′ end maturation module for nuclear non-coding RNAs
(Submitter supplied) Poly(A)-specific ribonuclease (PARN) and target of EGR1 protein 1 (TOE1) are nuclear granule-associated deadenylases, whose mutations are linked to multiple human diseases. Here, we applied mTAIL-seq and RNA sequencing (RNA-seq) to systematically identify the substrates of PARN and TOE1 and elucidate their molecular functions. We found that PARN and TOE1 do not modulate the length of mRNA poly(A) tails. 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/GSE111nnn/GSE111511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437251
Series		Accession: GSE111511	ID: 200111511

2171. The Promyelocytic Leukemia Zinc Finger Dependent Transcriptome during Human Endometrial Stromal Cell Decidualization
(Submitter supplied) RNA-sequencing of mRNA isolated from in vitro decidualizaing human endometrial stromal cells with or without siRNA-mediated knockdown of PLZF
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/GSE112nnn/GSE112362/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445798
Series		Accession: GSE112362	ID: 200112362

2172. A SIRT1-centered Circuitry Regulates Breast Cancer Stemness and Metastasis
(Submitter supplied) Deficiency of deacetylase SIRT1 or its downstream target PRRX1 promotes breast cancer stemness and metastasis. To explore the mechnisms of SIRT1 and its downstream target PRRX1 in breast cancer, we analysed the gene expressions in breast cancer BT549 cells with SIRT1 knockout or PRRX1 knockout or not.
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/GSE112nnn/GSE112365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445823
Series		Accession: GSE112365	ID: 200112365

2173. Choline Kinase Alpha (CHKα) as a Therapeutic Target in Pancreatic Ductal Adenocarcinoma: Expression, Predictive Value, and Sensitivity to Inhibitors
(Submitter supplied) Choline kinase α (CHKα) plays a crucial role in the regulation of membrane phospholipid synthesis and has oncogenic properties in vitro. We have analyzed the expression of CHKα in cell lines derived from pancreatic ductal adenocarcinoma (PDAC) and have found increased CHKα expression, associated with differentiation. CHKα protein expression was directly correlated with sensitivity to MN58b, a CHKα inhibitor that reduced cell growth through the induction of apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112335/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA445696
Series		Accession: GSE112335	ID: 200112335

2174. DNA methylation inhibitor in HCT116
(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 34 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108210/
Series		Accession: GSE108210	ID: 200108210

2175. Inhibitors of LSD1 target demethylase-independent activity to induce differentiation 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
Platforms: GPL16558 GPL18573 GPL16791 28 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63222/
Series		Accession: GSE63222	ID: 200063222

2176. Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [RNA-Seq experiments]
(Submitter supplied) To determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for monomethyl-, dimethyl- and trimethyl histone H3 modifications.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16558 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63217/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267008
Series		Accession: GSE63217	ID: 200063217

2177. Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Genome variation profiling by SNP array; SNP genotyping by SNP array; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by array; Methylation profiling by genome tiling array
4 related Platforms 52 Samples
FTP download: GEO (CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86260/
Series		Accession: GSE86260	ID: 200086260

2178. Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [RNA-seq]
(Submitter supplied) Cancer Associated Fibroblasts (CAFs) play an active role in tumourigenesis. It is unknown how the permanent phenotypic changes in CAFs are encoded at the molecular level. Here we use whole genome sequencing and microarray analysis to interrogate the epigenome, transcriptome and genome of patient-matched CAF and non-malignant prostate fibroblast (NPF) cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85606/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338944
Series		Accession: GSE85606	ID: 200085606

2179. Next Generation Sequencing Facilitates Quantitative of Transcriptomes in Various Cells Treated with or without LD100 and siRNA of SOD1
(Submitter supplied) Purpose: mRNA-sequencing has revolutionized systems-based analysis of cellular pathways. The goals of this study are to systemically research the biological functions of SOD1 in ROS signaling pathway using specific SOD1 inhibitor-LD100 and its validated siRNA.  Methods: We reported the mRNA-sequencing data of HeLa cells (designated as C), LD100-treated HeLa cells (L), SOD1 knockdown HeLa cells (S), DU145 cells (DC), LD100-treated DU145 cells (DL), RWPE-1 cells (RC) and LD100-treated RWPE-1 cells (RL). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112007/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438935
Series		Accession: GSE112007	ID: 200112007

2180. Modulation of ESRP2 and MBNL2 in normal kidney and clear cell renal cell carcinoma cell lines for analysis of stability programs
(Submitter supplied) While analyzing mRNA expression profiles of clear cell renal cell carcinoma (ccRCC) tumors, we found that the mRNAs that are bound at their 3' UTRs by muscleblind-like splicing regulator 2 (Mbnl2) and epithelial splicing regulatory protein 2 (ESRP2) are up-regulated in tumor compared to patient-matched normal tissues. Given that MBNL2 increases the stability of its targets and ESRP2 destabilizes its targets, we predicted that, in ccRCC tumors, MBNL2 activity increases, while ESRP2 activity decreases. 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/GSE83nnn/GSE83999/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327769
Series		Accession: GSE83999	ID: 200083999

2181. The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin
(Submitter supplied) The neurobiological functions of a number of kinases expressed in the brain are unknown.  Here, we report new findings on DCLK3 (Doublecortin-like kinase 3) which is preferentially expressed in neurons in the striatum and dentate gyrus. Its function has never been investigated. DCLK3 expression is markedly reduced in Huntington's disease. Recent data obtained in studies related to cancer suggest DCLK3 could have anti-apoptotic effect. 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/GSE104nnn/GSE104091/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA408232
Series		Accession: GSE104091	ID: 200104091

2182. RNA-Seq of fibrosarcoma with ESCC case
(Submitter supplied) Analysis of a fibrosarcoma with ESCC case at transcriptome level
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/GSE112nnn/GSE112083/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA439259
Series		Accession: GSE112083	ID: 200112083

2183. Comprehensive comparative analysis of 5’ end RNA sequencing methods
(Submitter supplied) RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5’ ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods – testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL15520 GPL16791 19 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103486/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401781
Series		Accession: GSE103486	ID: 200103486

2184. Gene expression analysis upon mtDNA depletion
(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; Methylation profiling by array
4 related Platforms 108 Samples
FTP download: GEO (BW, CEL, CHP, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100134/
Series		Accession: GSE100134	ID: 200100134

2185. HPV
(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
Platforms: GPL20148 GPL16791 181 Samples
FTP download: GEO (BED, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112027/
Series		Accession: GSE112027	ID: 200112027

2186. A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (RNA-Seq)
(Submitter supplied) The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 76 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112026/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438981
Series		Accession: GSE112026	ID: 200112026

2187. Hijacking of stress response machinery by oncogenes in acute leukaemia
(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: GPL11154 17 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90717/
Series		Accession: GSE90717	ID: 200090717

2188. Hijacking of stress response machinery by oncogenes in acute leukaemia [RNA-seq]
(Submitter supplied) Our data demonstrate binding of NOTCH1 on the promoters of HSF1 and HSF1 targets. We performed RNA-seq upon control conditions, inhibition of the NOTCH1 pathway by gSI, HSF1 knockdown and combination of HSF1 knockdown and gSI treatment. Our results show that NOTCH1 regulates the expression of heat shock response genes. Moreover, combination of HSF1 downregulation and gSI treatment further decreased the expression of heat shock response genes compared to single treatments.
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/GSE90nnn/GSE90715/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355574
Series		Accession: GSE90715	ID: 200090715

2189. IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors
(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: GPL15456 GPL11154 17 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109605/
Series		Accession: GSE109605	ID: 200109605

2190. IGF2BP1 enhances an aggressive tumor cell phenotype by impairing miRNA-directed downregulation of oncogenic factors [mRNA]
(Submitter supplied) The oncofetal IGF2 mRNA binding protein (IGF2BP) family modulates tumor cell properties but IGF2BP paralogue-specific roles remain poorly understood. We demonstrate that phenotypic roles of IGF2BPs vary in a cancer cell-dependent manner. However, only IGF2BP1 shows oncogenic potential in all cancer cells analyzed. Consistently, only IGF2BP1 expression is associated with poor prognosis in ovarian carcinoma and promotes all oncogenic properties analyzed in ovarian cancer-derived tumor cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 12 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109604/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431461
Series		Accession: GSE109604	ID: 200109604

2191. Discovering the interactions between circRNAs and RNA-binding proteins from RNA-seq and CLIP-seq data
(Submitter supplied) Although tens of thousands of circular RNAs (circRNAs) have been identified in mammalian genomes, only a few have been functionally characterized. Here, we report a new approach, circScan, to identify regulatory interactions between circRNAs and RNA-binding proteins (RBPs). Our method identifies back-splicing reads from crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq) data. 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/GSE97nnn/GSE97382/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381599
Series		Accession: GSE97382	ID: 200097382

2192. Gene expression alterations of pancreatic intraepithlial neoplasia
(Submitter supplied) Gene expression data from the RNA sequencing of laser microdissected pancreatic intraepithelial neoplasia and pancreatic normal ducts.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL16558 21 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96784/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379627
Series		Accession: GSE96784	ID: 200096784

2193. Nickel exposure induces persistent mesenchymal phenotype in human lung epithelial cells through epigenetic activation of ZEB1
(Submitter supplied) Purpose: Environmentally induced diseases, including cancer typically develop long after the exposure has occurred. However, most of the toxicological studies are conducted during active exposure. Therefore, environmental exposure-induced adverse effects that persist after cessation of exposure is poorly understood. Methods: Immortalized human bronchial epithelial cells (BEAS-2B) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Cellgro) supplemented with 1% Penicillin Streptomycin and 10% Fetal Bovine Serum (FBS, Atlanta Biologicals) at 37 degree C and 5 % CO2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95180/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376286
Series		Accession: GSE95180	ID: 200095180

2194. Transcriptome-wide HITS-CLIP of Quaking (QKI) in TGF-Beta-treated HMLE (Mesenchymal-like) cells
(Submitter supplied) Members of the miR-200 family are critical gatekeepers of the epithelial state, restraining expression of pro-mesenchymal genes that drive epithelial-mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR-200c and another epithelial-enriched miRNA, miR-375, exert widespread control of alternative splicing in cancer cells. This is achieved by their strong suppression of the RNA binding protein Quaking (QKI), which is required to mediate the splicing changes regulated by these miRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 9 Samples
FTP download: GEO (BED, BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111188/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436149
Series		Accession: GSE111188	ID: 200111188

2195. The roles of CSE1L in epigenetic silencing
(Submitter supplied) Epigenetic silencing can be mediated by various mechanisms and many regulators remain to be identified. We identified CSE1L as a factor essential for silencing of the reporter gene and a fraction of endogenous methylated genes. CSE1L depletion did not cause DNA demethylation or increase of global histone acetylation. Nevertheless, these methylated genes derepressed by CSE1L depletion largely overlapped with methylated genes that were also reactivated by treatment of histone deacetylase inhibitors (HDACi).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL23227 GPL20795 GPL20301 30 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379938
Series		Accession: GSE96852	ID: 200096852

2196. Recognition of RNA N6-methyadenosine by IGF2BP proteins Enhances mRNA Stability
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 44 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90686/
Series		Accession: GSE90686	ID: 200090686

2197. IGF2BP proteins Enhance mRNA stability
(Submitter supplied) To evaluate the effect of IGF2BPs on mRNA stability and gene expression output, we conducted RNA-seq in individual IGF2BP knockdown and control HepG2 cells with or without actinomycin D treatment. Our RNA-seq and RNA stability profiling revealed that IGF2BPs were involved in RNA stability regulation and contributed to the stabilization of the transcriptome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 30 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90684/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355385
Series		Accession: GSE90684	ID: 200090684

2198. CRISPR/Cas9-mediated ASXL1 mutation in U937 cells perturbs myeloid differentiation
(Submitter supplied) Purpose: Recurrent ASXL1 mutations are frequently observed in all spectrums of myeloid malignancies and published data suggests that ASXL1 mutations may be involved in leukemic transformation as a tumor suppressor. Yet the molecular mechanisms of cell desitiny regulated by ASXL1 are  to be further delineated. Methods: mRNA profiles of wild-type (WT) and CRISPR/Cas9 induced ASXL1 mutated U937 cell lines were generated by next generation sequencing, using Illumina HiSeq2500. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98104/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384005
Series		Accession: GSE98104	ID: 200098104

2199. mRNA-seq Analysis of Transcriptomes of the PC9R and PC9 cells
(Submitter supplied) The goals of this study is to compare the whole genome transcriptome of gefitinib-resistant NSCLC cell line (PC9R) with its gefitinib-sensitive counterpart (PC9) using RNA-seq tecnology Methods: Genome-wide mRNA profiles of the PC9R and PC9 cells were generated by deep sequencing, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed in the following steps: 1) RNA-seq reads were aligned to the hg19 genome assembly using TopHat (http://bioinformatics.oxfordjournals.org/content/25/9/1105.short) with the default parameters; 2) Expression index was generated using GFOLD V1.0.9 job count (http://bioinformatics.oxfordjournals.org/content/early/2012/08/23/bioinformatics.bts515); 3) Differential expression were calculated using GFOLD V1.0.9 job diff. 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/GSE74nnn/GSE74253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299577
Series		Accession: GSE74253	ID: 200074253

2200. RNA-seq analysis of colorectal cancer cell line (CRC) SW1116 overexpressed POLR1D
(Submitter supplied) Gene expression profiles were generated for CRC cell line SW1116 overexpressed POLR1D and empty vector to explore the effect of POLR1D on colorectal cancer cell line SW1116.
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/GSE111nnn/GSE111741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA438017
Series		Accession: GSE111741	ID: 200111741

2201. Metastasis 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; Genome variation profiling by SNP array
Platforms: GPL18460 GPL13829 24 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111706/
Series		Accession: GSE111706	ID: 200111706

2202. Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial 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: GPL16791 23 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109893/
Series		Accession: GSE109893	ID: 200109893

2203. Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer [RNA-seq]
(Submitter supplied) Steroid hormone receptors are simultaneously active in many tissues and capable of altering each other's function. Estrogen receptor ɑ (ER) and glucocorticoid receptor (GR) are expressed in the uterus and their ligands have opposing effects on uterine growth. In endometrial tumors expressing high levels of ER, we surprisingly found that expression of GR is associated with poor prognosis. Dexamethasone reduced normal uterine growth in vivo; however, this growth inhibition was abolished in estrogen-induced endometrial hyperplasia. 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/GSE109892/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432245
Series		Accession: GSE109892	ID: 200109892

2204. Effect of CBL0137 on nascent transcription in HT1080 cells [RNA-seq]
(Submitter supplied) Small molecule curaxin CBL0137 has broad anti-cancer activity in different preclinical models. It interferes with histone-DNA interactions via binding to DNA without causing DNA damage. It resposents first in class "chromatin damaging" agent without genotoxic properties. Its effect on the transcription in human tumor cells was evaluated. DNA-targeting small molecules are widely used for anticancer therapy based on their ability to induce cell death, presumably via DNA damage. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107633/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420940
Series		Accession: GSE107633	ID: 200107633

2205. LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies 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: GPL18573 34 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109493/
Series		Accession: GSE109493	ID: 200109493

2206. LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies in acute myeloid leukemia (RNA-Seq)
(Submitter supplied) Transcriptome analysis by high throughput sequencing
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/GSE109nnn/GSE109491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431335
Series		Accession: GSE109491	ID: 200109491

2207. RING-finger protein 6 amplification activates JAK/STAT3 pathway by modifying SHP-1 ubiquitylation and associates with poor outcome in colorectal cancer
(Submitter supplied) To elucidate whether  RNF6 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  RNF6 siRNA and control siRNA transfectants.
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/GSE107980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422102
Series		Accession: GSE107980	ID: 200107980

2208. Pancreatic tumor microenvironment confers highly malignant properties on pancreatic cancer cells
(Submitter supplied) Tumor microenvironment plays a pivotal role in cancer progression; however, little is known regarding how differences in the microenvironment affect characteristics of cancer cells. Here, we investigated the effects of tumor microenvironment on cancer cells by using mouse tumor models. After 3 cycles of inoculation and extraction of human pancreatic cancer cells, including SUIT-2 and Panc-1 cells, from tumors, distinct cancer cell lines were established; 3P cells from the pancreas obtained using the orthotopic tumor model, and 3sc cells from subcutaneous tissue obtained using the subcutaneous tumor model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107960/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422050
Series		Accession: GSE107960	ID: 200107960

2209. Transcriptomic sequencing after HOXA9 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, Homeobox A9 (HOXA9), a direct target of onco-miR-365, was identified to be significantly down-regulated in CSCC tumors and cell lines. We conducted RNA sequencing to characterize gene expression changes in HOXA9-silenced cutaneous squamous cell carcinoma cells（A431）.
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/GSE100nnn/GSE100144/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390836
Series		Accession: GSE100144	ID: 200100144

2210. Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 3273]
(Submitter supplied) PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 3409 Samples
FTP download: GEO (CSV, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96058/
Series		Accession: GSE96058	ID: 200096058

2211. Tracking of dCas9-methyltransferase footprints
(Submitter supplied) In normal mammalian development cytosine methylation is essential, and is directed to specific regions of the genome. Despite notable advances in mapping the genome-wide distribution, studying the direct contribution of DNA methylation to gene regulation has been limited by the lack of tools for its precise manipulation. Thus, combining the targeting capability of CRISPR/Cas9 systems with an epigenetic modifier has attracted interest in the scientific community. more...
Organism:	Mus musculus; Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 52 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87757/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA347354
Series		Accession: GSE87757	ID: 200087757

2212. Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [superseries]
(Submitter supplied) This SuperSeries is composed of the SubSeries GSE81538 [cohort 405] and GSE96058 [cohort 3273] linked to below.  PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 3814 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81540/
Series		Accession: GSE81540	ID: 200081540

2213. Clinical Value of RNA Sequencing–Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network—Breast Initiative [cohort 405]
(Submitter supplied) PURPOSE In early breast cancer (BC), five conventional biomarkers—estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG)—are used to determine prognosis and treatment. We aimed to develop classifiers for these biomarkers that were based on tumor mRNA sequencing (RNA-seq), compare classification performance, and test whether such predictors could add value for risk stratification. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 405 Samples
FTP download: GEO (CSV, GTF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81538/
Series		Accession: GSE81538	ID: 200081538

2214. The LINC01138 Drives Malignancies via Activating Arginine Methyltransferase 5 in Hepatocellular Carcinoma
(Submitter supplied) Our study have demonstrated LINC01138 acts as an oncogenic driver that promotes cell proliferation, tumourigenicity, tumour invasion and metastasis through physically interacting with Arginine Methyltransferase 5 (PRMT5) in HCC cells. In order to investigate the related signaling pathways regulated by LINC01138 or PRMT5, we performed the unbiased transcriptome profiling using high-throughput RNA sequencing in SMMC-7721 cells transfected with si-LINC01138 or si-PRMT5. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111655/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437713
Series		Accession: GSE111655	ID: 200111655

2215. RNA sequencing data from triple-negative breast cancer patient-derived xenografts (PDX)
(Submitter supplied) RNAseq was performed on WHIM2 and WHIM30 PDX mammary tumors, brain metastases, and single cell suspensions over time.
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/GSE110nnn/GSE110626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434130
Series		Accession: GSE110626	ID: 200110626

2216. Synthetic lethality between ARID1A mutation and HDAC2 inhibition in ovarian cancer
(Submitter supplied) ARID1A, encoding a subunit of the SWI/SNF chromatin remodeling complex, is the most frequently mutated epigenetic regulators in human cancers.  ARID1A is mutated in over 50% ovarian clear cell carcinoma, a disease currently has no effective therapy.  Here we show that ARID1A-mutated ovarian cancer cells are selectively sensitive to inhibition of HDAC2 activity. HDAC2 interacts with EZH2 in an ARID1A status dependent manner. 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/GSE107201/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419301
Series		Accession: GSE107201	ID: 200107201

2217. BRCA1, R-loops and Recombination defects in Ewing's sarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL21290 GPL11154 79 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68847/
Series		Accession: GSE68847	ID: 200068847

2218. BRCA1, R-loops and Recombination defects in Ewing's sarcoma (RNA-seq)
(Submitter supplied) Ewing’s sarcoma family of tumors (ESFT) is an aggressive pediatric bone and soft tissue cancer. It is the prototypical example of mesenchymal tumors driven by a fusion oncogene involving the ewing sarcoma break point region 1 (EWSR1) gene, most frequently– EWS-FLI1. We have discovered that loss of EWSR1 leads to accumulation of R-loops, replication stress and impaired homologous recombination, recapitulating breast cancer 1, early onset (BRCA1) deficiency. more...
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/GSE68nnn/GSE68836/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA283885
Series		Accession: GSE68836	ID: 200068836

2219. RNA-seq data of adipocytes co-cocultured with OVCAR5 in Boyden chamber (4d)
(Submitter supplied) We indirectly cocultured OVCAR5-RFP cells using a 0.45 micron Boyden chamber with or without adipocytes for 4 days, collected the RNA from adipocytes, and performed RNA-seq
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/GSE111nnn/GSE111538/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA437317
Series		Accession: GSE111538	ID: 200111538

2220. SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRDs_OE_RNA-seq)
(Submitter supplied) Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics of cancers including prostate cancer.  The E3 ubiquitin ligase adaptor protein speckle-type POZ protein (SPOP) is implicated in human prostate cancers due to its frequent mutation.  Here we demonstrate that SPOP binds to the BET proteins BRD2, BRD3 and BRD4.  Wild-type SPOP, but not prostate cancer-associated mutants, promotes polyubiquitination and proteasome degradation of BET proteins by recognizing a common degron motif. 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/GSE98nnn/GSE98010/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383658
Series		Accession: GSE98010	ID: 200098010

2221. Glutaminolysis is a metabolic dependency in FLT3 ITD Acute Myeloid Leukemia unmasked by FLT3 Tyrosine Kinase Inhibition
(Submitter supplied) FLT3ITD are common mutations in Acute Myeloid Leukemia (AML) and carry a particularly bad prognosis. Although new generation FLT3 tyrosine kinase inhibitors (TKI) have shown promising results, the outcome of FLT3-mutated AML patients remains poor and demands the identification of novel, specific and validated therapeutic targets for this highly aggressive AML subtype. Utilizing an unbiased genome-wide CRISPR/Cas9 screen, we identify GLS, the first enzyme in glutamine metabolism, as synthetically lethal with FLT3 TKI treatment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105161/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414977
Series		Accession: GSE105161	ID: 200105161

2222. Chromatin structure alteration regulates key transcription factor expression during blood cell differentiation
(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: GPL16791 GPL11154 20 Samples
FTP download: GEO (BED, BROADPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93997/
Series		Accession: GSE93997	ID: 200093997

2223. Differential Gene Expression between ATRA treated and control HL-60 Cells [RNA-seq]
(Submitter supplied) These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis. Analysis revealed differential expressed genes in ATRA treated and control HL-60 cells. Changes of gene expression with topological associated domains (TADs) were showd to be correlated with chromatin structure alteration
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/GSE93nnn/GSE93996/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA363025
Series		Accession: GSE93996	ID: 200093996

2224. Identification and characterization of androgen receptor splice variants preferred bindings that drive 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: GPL11154 29 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80743/
Series		Accession: GSE80743	ID: 200080743

2225. Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [RNA-seq]
(Submitter supplied) Androgen receptor (AR) splice variants (ARVs) are implicated in developing castration-resistant (CR) prostate cancer (CRPC). Little is known about the ARV-mediated transcription program in CRPC. We identified ARV-preferred binding sites (ARV-PBS) and unique transcriptome in CRPC cells. ARVs preferentially bind to enhancers located in nucleosome-depleted regions with the full AR-response element (AREfull), while full-length AR (ARFL)-PBS are enhancers resided in closed chromatin regions with the composite FOXA1-nnnn-AREhalf motif. 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/GSE80nnn/GSE80741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319902
Series		Accession: GSE80741	ID: 200080741

2226. RNA-seq of SCLC PDX models treated with EP
(Submitter supplied) We report the correlation of transcript abundance with response to EP in 19 PDX models of SCLC
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 19 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110853/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434676
Series		Accession: GSE110853	ID: 200110853

2227. Gene Expression in Human Rhabdomyosarcoma
(Submitter supplied) Gene expression analysis identified unique transcriptional changes in rhabdomyosarcoma when compared with normal muscle.  Our studies focused on a gene called VANGL2 that regulated growth and self-renewal in embryonal rhabdomyosarcoma.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 106 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108022/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA238612
Series		Accession: GSE108022	ID: 200108022

2228. The regulartory role of ZCCHC24 in splicing machinery
(Submitter supplied) ZCCHC24, Zinc Finger, CCHC domain containing 24. Showed mesenchymal cell specific expression, but no known function or phenotype associated with it. It required for mesenchymal cell growth, KD in mesenchymal cells induces drastic growth arrest. Its role in splicing machinery is not known.
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/GSE66nnn/GSE66632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA277487
Series		Accession: GSE66632	ID: 200066632

2229. Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [RNA-Seq 2]
(Submitter supplied) The addressable pocket of a target protein is often not functionally relevant. This is particularly true for multidomain gene regulatory proteins, such as the bromodomain-containing transcriptional regulator TRIM24. TRIM24 has been posited as a dependency in numerous human cancers, yet potent and selective ligands for the TRIM24 bromodomain do not exert effective anti-proliferative responses. We therefore repositioned these probes as targeting features for heterobifunctional protein degraders.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 45 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106579/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417275
Series		Accession: GSE106579	ID: 200106579

2230. Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands
(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 69 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100573/
Series		Accession: GSE100573	ID: 200100573

2231. Functional TRIM24 degraders via conjugation of ineffectual bromodomain and VHL ligands [RNA-seq]
(Submitter supplied) The addressable pocket of a target protein is often not functionally relevant. This is particularly true for multidomain gene regulatory proteins, such as the bromodomain-containing transcriptional regulator TRIM24. TRIM24 has been posited as a dependency in numerous human cancers, yet potent and selective ligands for the TRIM24 bromodomain do not exert effective anti-proliferative responses. We therefore repositioned these probes as targeting features for heterobifunctional protein degraders.
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/GSE100nnn/GSE100572/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392162
Series		Accession: GSE100572	ID: 200100572

2232. GSF1243: RNA-seq data of adipocytes treated with DNMT1 inhibitor, guadecitabine (100nM), for 3 days
(Submitter supplied) Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE111nnn/GSE111305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436558
Series		Accession: GSE111305	ID: 200111305

2233. Transcriptional changes in glioma cells following treatment with 1-Benzyl-3-cetyl-2-methylimidazolium iodide (NH125), Tunicamycin, and 0.1% DMSO (in media)
(Submitter supplied) Purpose: Evaluate transcriptional changes in glioma derived stem cells, U251, and normal human astrocytes following treatment with NH125, Tunicamycin, or 0.1% DMSO Methods: Glioma derived stem cells, U251 and Normal Human Astrocytes were plated in individual dishes and treated with either 2.5 micromolar NH125, 1.0 mcg/mL Tunicamycin, or 0.1% DMSO (vehicle) for twenty-four hours followed by total RNA extraction, library preparation and next generation sequencing Results: Using our analysis pipeline we mapped our sequence reads to the reference genome GRCh38. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102505/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397903
Series		Accession: GSE102505	ID: 200102505

2234. The novel BETi BI 894999 represses super-enhancer associated transcription and synergizes with CDK9 inhibition in AML by induction of apoptosis
(Submitter supplied) Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for acute myeloid leukemia (AML) in preclinical models and are currently being evaluated in clinical trials. This work presents a novel potent and selective BET inhibitor (BI 894999), which has recently entered clinical trials (NCT02516553). In preclinical studies, this compound is highly active in AML cell lines, primary patient samples, and xenografts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18460 GPL18573 101 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101821/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395584
Series		Accession: GSE101821	ID: 200101821

2235. Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response
(Submitter supplied) Increasing evidence indicates that minor subpopulations intrinsic to androgen-independence are present in prostate cancer cells, poised to become clonal dominance under prolonged androgen-deprivation selection. To stratify different subpopulations, we conduct transcriptome profiling of 144 single LNCaP prostate cancer cells treated and untreated with androgen after cell cycle synchronization. At least eight subpopulations of LNCaP cells are identified, revealing a previously unappreciable level of cellular heterogeneity to androgen stimulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 147 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99795/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389624
Series		Accession: GSE99795	ID: 200099795

2236. RNAseq of CCRF-CEM, a T-cell acute lymphoblastic leukemia cell line, after knockdown with 2 control hairpins and 6 hairpins targeting the PRC2 complex.
(Submitter supplied) The data was used to study mechanisms of apoptosis resistance induced by loss of PRC2.
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/GSE95nnn/GSE95648/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377758
Series		Accession: GSE95648	ID: 200095648

2237. CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity
(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: GPL11154 GPL18573 8 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95645/
Series		Accession: GSE95645	ID: 200095645

2238. CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity [RNA-Seq]
(Submitter supplied) CARM1 is an arginine methyltransferase that asymmetrically dimethylates protein substrates on arginine residues. CARM1 is often overexpressed in cancers and stimulates growth.  However, clinically applicable therapeutic strategies based on CARM1 expression in cancer remains to be explored.  Here we show that epithelial ovarian cancer is among the cancers with the highest CARM1 amplification rates that predicates a shorter survival. 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/GSE95nnn/GSE95644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377752
Series		Accession: GSE95644	ID: 200095644

2239. transcriptome studies of BRD4 inhibitor BDF-1253 on renal clear carcinoma 786-O cells
(Submitter supplied) As an epigenetic reader, BRD4 is important for the recognition of acetylated lysines and regulation of transcription. As BRD4 regulates the expression of several survival genes, such as c-Myc and Bcl-2, which is vital for the survival of tumor cells, then it is closely involved in various kinds of cancers. Accumulating evidence has proven that BRD4 could serve as a novel anti-cancer pharmaceutical target, and small-molecular BRD4 inhibitors have promising potentials in the treatment of BRD4-related cancers and other diseases. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109870/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432221
Series		Accession: GSE109870	ID: 200109870

2240. The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma
(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 40 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108929/
Series		Accession: GSE108929	ID: 200108929

2241. The SS18-SSX oncoprotein hijacks KDM2B-PRC1.1 to drive synovial sarcoma [RNA-seq]
(Submitter supplied) Gene fusions arising from chromosomal translocations are key oncogenic drivers in soft tissue sarcomas but little is known about how they exert their oncogenic effects. Our study explores the molecular mechanisms by which the SS18-SSX fusion oncoprotein subverts epigenetic mechanisms of gene regulation to drive synovial sarcoma. Using functional genomics, we identify KDM2B – a histone demethylase and core component of a non-canonical Polycomb Repressive Complex 1 (PRC1.1) – as selectively required for sustaining synovial sarcoma cell transformation. 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/GSE108nnn/GSE108928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429315
Series		Accession: GSE108928	ID: 200108928

2242. Targeted enhancer activation by a subunit of the integrator complex
(Submitter supplied) We investigated the genomic occupancy of INTS13 during monocytic differentiation, in in vitro differentiated monocytes and a leukemia-derived cell line. We produced genome wide data for steady state RNA (total RNA-seq) and chromatin-associated RNA (chromatin RNA-seq). Further, we used ChIP-seq to examine genome-wide distribution of INTS13, INTS11, EGR1 and NAB2, as well as the changes in occupancy of  RNAPII, H3K4me1 and H3K27ac.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 53 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106359/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416461
Series		Accession: GSE106359	ID: 200106359

2243. The ARID1A tumor suppressor controls global transcription via pausing of RNA Polymerase II
(Submitter supplied) We investigated the genomic consequences of the depletion of the SWI/SNF subumit ARID1A, in an ovarian cancer derived model. We produced genome wide data for nascent RNA (GRO-seq) and steady state RNA (total RNA-seq). Further, we used ChIP-seq to examine genome-wide distribution of ARID1A, as well as the changes in occupancy of  RNAPII, H3K4me3 and H3K36me3. Finally we used ATAC-seq to investigate chromatin accessibility.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL18573 37 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413026
Series		Accession: GSE104545	ID: 200104545

2244. Super-enhancer analysis of human sarcomas reveals YAP1 control of NF-κB-dependent tumorigenesis
(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 9 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97297/
Series		Accession: GSE97297	ID: 200097297

2245. Super-enhancer analysis of human sarcomas reveals YAP1 control of NF-κB-dependent tumorigenesis [RNA-seq]
(Submitter supplied) Recent sequencing efforts have failed to identify consistent oncogenic driver mutations in most adult soft tissue sarcomas. Therefore, we investigated alternate genetic/epigenetic mechanisms underlying sarcomagenesis to facilitate development of novel therapeutics. Our previous work showed that deregulation of the Hippo pathway increases proliferation in many types of sarcoma. We have now identified the mechanism of Hippo-mediated sarcomagenesis using autochthonous mouse models, ChIP-seq (H3K27Ac) and super-enhancer (SE) analysis of human undifferentiated pleomorphic sarcoma (UPS), an aggressive muscle-derived tumor. 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/GSE97nnn/GSE97296/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381271
Series		Accession: GSE97296	ID: 200097296

2246. The effect of Abl kinases,or Ponatinib challenging on breast cancer cells' global transcriptome
(Submitter supplied) To gain insight into the signaling pathway(s) required for ABL1/ABL2-kinase activity or effected by Ponatinib treatment, we evaluated the consequences of single or double inactivation of ABL1/ABL2 cells, or Ponatinib treated cells on the transcriptome of breast cancer cells. To examine the consequences of depleting the ABL kinases, or Ponatinib treatment on the transcriptome of lung metastatic breast cancer cells we employed next generation sequencing (RNAseq) analysis. 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/GSE95nnn/GSE95079/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376006
Series		Accession: GSE95079	ID: 200095079

2247. RNA sequencing (RNA-SEQ) of 21 HBV-HCC patients with non-neoplastic liver and tumor tissues
(Submitter supplied) Purpose: Chronic Hepatitis B virus (HBV) infection leads to liver fibrosis which is a major risk factor in Hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. HBV genome can be inserted into human genome, and chronic inflammation may trigger somatic mutations. Several studies characterized HBV integration sites in HCC patients with regard to frequently occurring hotspots. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94660/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371753
Series		Accession: GSE94660	ID: 200094660

2248. Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Non-coding RNA profiling by array; Expression profiling by array; Expression profiling by high throughput sequencing
Platforms: GPL20115 GPL16791 GPL22722 55 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90741/
Series		Accession: GSE90741	ID: 200090741

2249. Genome wide characterization of a STAT1-independent antiviral and immunoregulatory transcriptional program induced by IFNβ and TNFα reveals non-canonical STAT2 and IRF9 pathways
(Submitter supplied) Interferon (IFN) β and Tumor Necrosis Factor (TNF) α are key players in immunity against pathogens as well as in the development of autoinflammatory and autoimmune diseases. Accordingly, their molecular pathways have attracted much interest as therapeutic targets. Compelling evidence has shown that the antiviral and inflammatory transcriptional response induced by IFNβ is reprogrammed by crosstalk with TNFα. more...
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/GSE111nnn/GSE111195/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436141
Series		Accession: GSE111195	ID: 200111195

2250. Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes
(Submitter supplied) Methods:  mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
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/GSE111nnn/GSE111168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA436090
Series		Accession: GSE111168	ID: 200111168

2251. Single cell profiling of 3 Human Lung Adenocarcinoma cell lines.
(Submitter supplied) An equal mixture of cells from the 3 Human Lung Adenocarcinoma cell lines (H2228, NCI-H1975 and HCC827) were processed on the Chromium 3' single cell platform (10X Genomics) and sequenced on an Illumina NextSeq 500. FASTQ data were preprocessed using both scPipe and CellRanger.
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/GSE111nnn/GSE111108/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA435946
Series		Accession: GSE111108	ID: 200111108

2252. Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following anti-angiogenic treatment
(Submitter supplied) To understand tumor stromal cell heterogeneity focusing on tumor endothelial cells and tumor-associated fibroblasts, we isolated single cells from COLO205 tumor xenograft grown sub-cutaneously in SCID mice. To enrich stromal cell content, we removed vast majority of tumor cells by a depletion protocol using anti-CD24 and anti-E-Cadherin antibodies. The remaining single cells were profiled by single cell RNAseq
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL19415 16 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110501/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433865
Series		Accession: GSE110501	ID: 200110501

2253. Mechanistic insights into anti-cancer properties of oligomeric proanthocyanidins from grape seeds in colorectal cancer
(Submitter supplied) Although the anti-cancer properties of Oligomeric Proanthocyanidins (OPCs) from grape seeds has been well recognized, the molecular mechanisms by which they exert anti-cancer effects are poorly understood. In this study, through comprehensive RNA-sequencing based gene-expression profiling in multiple colorectal cancer cell lines, we for the first time illuminate the genome-wide effects of OPCs from grape seeds in colorectal cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 30 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109607/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431467
Series		Accession: GSE109607	ID: 200109607

2254. PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage
(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
Platform: GPL17303 20 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101776/
Series		Accession: GSE101776	ID: 200101776

2255. PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [RNA-Seq]
(Submitter supplied) Down-regulation (DR) of PREP1 (aka PKNOX1) tumor suppressor induces H2Ax foci in human fibroblasts. Here we have analyzed the effect of PREP1 DR on DNA replication using cell cycle analysis, Repliseq, DNA combing, ChIP-seq, RNA-seq and immunofluorescence (IF). In human cells, PREP1 DR similarly affects both the rate of DNA replication and the progression of cells through the S phase. Genome wide, PREP1 DR induces late to early DNA replication shifts in normally late-replicated genomic regions amounting to 25% of the genome, in addition to unscheduled origins firing. 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/GSE101nnn/GSE101774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395426
Series		Accession: GSE101774	ID: 200101774

2256. Selective modulation of inflammatory Natural Killer (NK) cell phenotypes following histone H3K27 demethylase inhibition [RNA-Seq]
(Submitter supplied) Natural Killer cells are innate lymphocytes, participate in immune surveillance and elimination of stressed or transformed cells and critically shape the inflammatory cytokine environment to interact with cells of the innate and adaptive immune system, including macrophages, dendritic and Tcells. By performing a focused compound library screening, further validated by knockdown approaches, we here identify Jumonji-type histone 3 lysine 27 (H3K27) demethylases as key regulators of cytokine production in various human NK cell subsets. 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/GSE89nnn/GSE89484/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352350
Series		Accession: GSE89484	ID: 200089484

2257. Single cell transcriptional dynamics of flavivirus infection
(Submitter supplied) Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2260 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110496/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433871
Series		Accession: GSE110496	ID: 200110496

2258. Resistance to BET inhibitor leads to new therapeutic vulnerabilities in castration resistant prostate cancer
(Submitter supplied) BRD4 plays a major role in the transcription networks orchestrated by androgen receptor (AR) in castration resistant prostate cancer (CRPC) cells. Bromodomain and extraterminal protein (BET) inhibitors displace BRD4 protein from chromatin, resulting in the inhibition of oncogenic transcriptional programs. Several BET inhibitors (BETi) are currently being evaluated in clinical trials for a variety of malignancies, including CRPC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400161
Series		Accession: GSE103082	ID: 200103082

2259. Synergistic activity of BET inhibitor BI 894999 with PLK inhibitor volasertib in AML in vitro and in vivo
(Submitter supplied) Interactions between a new potent Bromodomain and extraterminal domain (BET) inhibitor BI 894999 and the polo-like kinase (PLK) inhibitor volasertib were studied in acute myeloid leukemia cell lines in vitro and in vivo. We provide data for the distinct mechanisms of action of these two compounds with a potential utility in AML based on gene expression, cell cycle profile and modulation of PD biomarkers such as MYC and HEXIM1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 36 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103068/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400080
Series		Accession: GSE103068	ID: 200103068

2260. RNA Seq analysis of pancreatic beta cell transcriptome during dedifferentiation
(Submitter supplied) We report RNA Seq analysis using Illumina nextSeq500 of human beta cells EndoC-BH1 treated with FGF2 to induce dedifferentiation. FGF2 treatment induced dedifferentiation of EndoC-BH1 cells. Indeed, we observed a strong decrease in expression of β-cell markers, (INS, MAFB, SLC2A2, SLC30A8 and GCK).  Opposingly, we identifed positive markers of human β cell dedifferentiation, as attested by increased expression of mature β-cell disallowed transcription factors (MYC, HES1, SOX9 and NEUROG3). more...
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/GSE103383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401709
Series		Accession: GSE103383	ID: 200103383

2261. Expression data in LoVo cells treated with MEK inhibitor
(Submitter supplied) We analyzed publicly available mucosal gene expression data from Crohn's disease (CD) patients pre- and post-infliximab therapy and found that a series of gene expression signature that remains abnormal even if patients achieve clinical remission. Using CMap approach to discover novel therapeutic target for untreatable mechanism of anti-TNFa mAb therapy, we have identified MEK inhibitor exhibiting negatively-correlated effects on reference signature match infliximab therapy untreatable signature. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422292
Series		Accession: GSE108050	ID: 200108050

2262. Expression profile of Gastro-Entero-Pancreatic Neuroendocrine Tumors (GEP-NET)
(Submitter supplied) Expression profile of human GEP-NET tumors, including 113 fresh frozen biopsies of primary and metastatic tumours originating from pancreas (P-NET, 83 primary and 30 metastasis), 81 from small intestine (SI-NET, 44 primary and 37 metastasis), and 18 from rectum (RE-NET, 3 primary and 15 metastasis).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 212 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98894/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386518
Series		Accession: GSE98894	ID: 200098894

2263. Consequences of Ribosomal Protein Haploinsufficiency in Human Hematopoiesis
(Submitter supplied) Ribosomal protein haploinsufficiency (RPH) underlies diverse human diseases with distinct and specific phenotypes, including Diamond-Blackfan anemia (DBA). Although multiple mechanisms have been proposed for the erythroid-specific hematopoietic defects observed in DBA, only recently has the role of selectively impaired translation been highlighted in these phenotypes. Exactly how and to what extent this impairment of translation occurs is currently unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 14 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350543
Series		Accession: GSE89183	ID: 200089183

2264. Knockout human reveal an essential role for Paternally Expressed 10 (PEG10) in JEG3 cell line development
(Submitter supplied) Tissue- and cell-type specific regulators of alternative splicing (AS) are an essential layer of posttranscriptional gene regulation necessary for normal cellular function, patterning, and development. Here we report the Paternally Expressed 10 (PEG10) are required for patterning of multiple organs, with loss of PEG10, resulting in increasingly severe phenotypes.
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/GSE66nnn/GSE66304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA276466
Series		Accession: GSE66304	ID: 200066304

2265. TRIM24 is an oncogenic transcriptional co-activator of STAT3 in glioblastoma
(Submitter supplied) Aberrant amplication and mutations of epidermal growth factor receptor (EGFR) are the most common oncogenic events in glioblastoma (GBM), but the mechanisms by which they promote aggressive pathogenesis are not well understood. Here, we determined that non-canonical histone signature acetylated H3 lysine 23 (H3K23ac)-binding protein tripartite motif-containing 24 (TRIM24) is upregulated in clinical specimens of glioblastoma and is required for EGFR-driven tumorigenesis.
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/GSE95nnn/GSE95386/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376867
Series		Accession: GSE95386	ID: 200095386

2266. Peptidomimetic blockade of MYB 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 29 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94242/
Series		Accession: GSE94242	ID: 200094242

2267. Peptidomimetic blockade of MYB in acute myeloid leukemia [RNA-seq]
(Submitter supplied) Aberrant gene expression is a hallmark of acute leukemias. However, therapeutic strategies for its blockade are generally lacking, in large part due to the pharmacologic challenges of drugging transcription factors. MYB-driven gene trans-activation with CREB-binding protein (CBP) is required for the initiation and maintenance of a variety of acute lymphoblastic and myeloid leukemias, including refractory MLL-rearranged leukemias. 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/GSE94nnn/GSE94241/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369119
Series		Accession: GSE94241	ID: 200094241

2268. Characterizing the epigenome of glioma 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; Methylation profiling by array; Methylation profiling by high throughput sequencing
Platforms: GPL21145 GPL13534 GPL16791 157 Samples
FTP download: GEO (BED, BW, FPKM_TRACKING, IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92469/
Series		Accession: GSE92469	ID: 200092469

2269. Characterizing the epigenome of glioma stem cells (RNA-Seq)
(Submitter supplied) Glioma initiating cells/stem cells exist in the bulk tumor of glioblastoma. This cell population contributes to the frequent resistances toward radiation/chemotherapy, aggressiveness of adult brain cancer and increased recurrence rate. Targeting stem cell population becomes one the most promising and permissive therapeutic strategies. We isolated glioma stem cells from patient-derived xenografts and profiled their epigenomic features, including 4 different DNA marks and 2 enhancer marks, and transcriptome in these in vitro cultured cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (BW, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92459/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357610
Series		Accession: GSE92459	ID: 200092459

2270. SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia [RNA-seq]
(Submitter supplied) We identified novel recurrent genetic lesions in T-PLL affecting genes involved in JAK/STAT signaling (PTPRC), epigenetic regulation (PRDM2), or DNA damage repair (SAMHD1, PARP10, HERC1, HERC2). Mutations of the tumor suppressor gene SAMHD1 causing amino-acid exchanges or protein truncations as well as copy number variations in SAMHD1 were seen in 20% of cases.
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/GSE100nnn/GSE100882/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395211
Series		Accession: GSE100882	ID: 200100882

2271. RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with pancreatic carcinoma
(Submitter supplied) Exosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequencing (RNA-seq). 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/GSE100nnn/GSE100232/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391134
Series		Accession: GSE100232	ID: 200100232

2272. RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with hepatocellular carcinoma
(Submitter supplied) Exosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequencing (RNA-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100207/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390991
Series		Accession: GSE100207	ID: 200100207

2273. RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with colorectal carcinoma
(Submitter supplied) Exosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequencing (RNA-seq). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100063/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390615
Series		Accession: GSE100063	ID: 200100063

2274. RNA-Seq of treatment response of platinum sensitive and platinum resistant ovarian cancer cells
(Submitter supplied) Resistance to platinum-based chemotherapy is a clinical challenge in the treatment of ovarian cancer (OC) and limits survival. Therefore, innovative drugs against platinum-resistance are urgently needed. Our therapeutic concept is based on the conjugation of two chemotherapeutic compounds to a monotherapeutic pro-drug, which is taken up by cancer cells and cleaved into active cytostatic metabolites. 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/GSE98nnn/GSE98230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384352
Series		Accession: GSE98230	ID: 200098230

2275. DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors
(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
Platforms: GPL20301 GPL21145 50 Samples
FTP download: GEO (IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95462/
Series		Accession: GSE95462	ID: 200095462

2276. DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [RNA-seq]
(Submitter supplied) Using genome-wide approaches, we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377162
Series		Accession: GSE95461	ID: 200095461

2277. RNA sequencing of prostate cancers reveal insights on the prognostic significance of visibility on multi-parametric MRI
(Submitter supplied) Not all prostate cancers are visible on multiparametric MRI. The biologic basis and clinical implication of MRI visibility are unknown. We sought to identify genes associated with prognosis and MRI visibility.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95369/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376773
Series		Accession: GSE95369	ID: 200095369

2278. Identification of the RB loss-induced transcriptome and E2F1 cistrome in 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 14 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94959/
Series		Accession: GSE94959	ID: 200094959

2279. Somatic PRDM2 c.4459delA mutations in colorectal cancers control histone methylation and tumor growth
(Submitter supplied) Purpose: To identify the contribution of PRDM2 c.4459delA mutation to colorectal tumorigenesis Methods: We employed rAAV-mediated genome editing to correct somatic PRDM2 c.4459delA mutation in homozygously mutated cell line. Using next-generation sequencing we have compared transcriptional profile of parental and PRDM2-corrected cells. Results: RNA-seq profiling revealed that several hallmark cancer gene sets are affected by PRDM2 c.4459delA
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/GSE80nnn/GSE80033/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317667
Series		Accession: GSE80033	ID: 200080033

2280. Androgen Receptor-regulated genes in prostate cancer cells
(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: GPL4133 GPL11154 30 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110905/
Series		Accession: GSE110905	ID: 200110905

2281. RNA-seq profiling identifies Androgen Receptor-regulated genes in prostate cancer cells
(Submitter supplied) The goal of this analysis is to profile AR-regulated genes, especially non-coding RNAs in three androgen sensitive prostate cancer cell lines, MDA-PCA-2B, LNCaP and VCaP. The two cell lines were serum-starved first, followed by dihydrotestosterone (DHT) stimulation or treated with Enzalutamide (AR inhibitor) without starvation. Transcriptome profiling was generated by RNA-sequencing from polyA-selected RNA. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 17 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434757
Series		Accession: GSE110903	ID: 200110903

2282. Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding
(Submitter supplied) To facilitate scalable profiling of single cells, we developed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL24625 GPL21626 6 Samples
FTP download: GEO (MAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110823/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434658
Series		Accession: GSE110823	ID: 200110823

2283. RNA sequencing Facilitates Quantitative Analysis of luminal breast cancer cells and basal breast cancer cells Transcriptomes
(Submitter supplied) We conduct transcriptome comparison of lumianl breast cancer cells and basal cells to gain genomic insights on the biological processes. More than 3000 known genes were found changed in basal breast cancer cells. Ingenuity Pathway Analysis _IPA_ and Gene Set Enrichment Analysis _GSEA_ show that the prominent altered pathways in basal cells are related to regulation of actin-based motility, JAK/STAT3 signaling pathway.
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/GSE110nnn/GSE110810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434599
Series		Accession: GSE110810	ID: 200110810

2284. Gene Expression of Small Cell Carcinoma of the Ovary, hypercalcemic type.
(Submitter supplied) Small cell carcinoma of the ovary-hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer afflicting young women at a median age of 24 years. SCCOHTs are characterized by loss of protein expression of SWI/SNF chromatin remodeling ATPases SMARCA4 and SMARCA2 through mutation and epigenetic silencing, respectively. This study aims to establish gene expression profiles of this cancer through RNA-Seq of four pathologically confirmed cases of SCCOHT tumors.
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/GSE109nnn/GSE109919/
Series		Accession: GSE109919	ID: 200109919

2285. Profiling of differential RNAs in alpha amanitin treated SORBS2-depleted ovarian cancer cells and control-treated SORBS2-depleted
(Submitter supplied) In this study, we examined the differential RNA profile of alpha  amanitin-treated SORBS2-depleted ovarian cancer cells compared with control-treated SORBS2-depleted 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/GSE101nnn/GSE101595/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394908
Series		Accession: GSE101595	ID: 200101595

2286. Profiling of differential RNAs in SORBS2-depleted ovarian cancer cells and control cells
(Submitter supplied) In this study, we examined the differential RNA profile of SORBS2-depleted ovarian cancer cells compared with control 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/GSE101nnn/GSE101594/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394909
Series		Accession: GSE101594	ID: 200101594

2287. COMBINING BET AND MEK INHIBITORS SYNERGISTICALLY TARGETS   NRAS MUTANT MELANOMA
(Submitter supplied) Nearly 30% of all malignant melanomas harbor somatic mutations in NRAS.  However, there are currently no effective targeted therapies for this tumor type. The bromodomain and extra terminal domain (BET) family of proteins are transcriptional regulators that serve as scaffolds to facilitate gene transcription by binding to acetylated lysine residues in the N-terminal tail of histones.  BET/BRD proteins have emerged as therapeutic targets in a broad range of tumors. more...
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/GSE95nnn/GSE95153/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376198
Series		Accession: GSE95153	ID: 200095153

2288. Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL23642 52 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100695/
Series		Accession: GSE100695	ID: 200100695

2289. Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors [Human cell line RNA-seq]
(Submitter supplied) Understanding the specific cell populations responsible for propagation of leukemia is an important step for development of effective targeted therapies. Recently, the lymphoid-primed multipotent progenitor (LMPP) has been proposed to be a key propagating population in acute myeloid leukemia (AML; PMID 21251617). We have also shown that LMPPs share many functional and gene expression properties with early thymic progenitors (ETPs; PMID 22344248). 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/GSE100nnn/GSE100694/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392682
Series		Accession: GSE100694	ID: 200100694

2290. Identification of the RB loss-induced transcriptome in prostate cancer [RNA]
(Submitter supplied) The retinoblastoma protein (RB) is preferentially lost in the progression to castrate resistant prostate cancer (CRPC).  However, the alterations associated with such loss have been scantly described.  The current study aims to provide molecular mechanisms underlying Rb loss-driven CRPC phenotypes
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/GSE94nnn/GSE94863/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374662
Series		Accession: GSE94863	ID: 200094863

2291. AR Expression in Breast Cancer CTCs Associates with Bone Metastases
(Submitter supplied) Molecular drivers underlying bone metastases in human cancer are not well understood, in part due to constraints in bone tissue sampling. Here, we undertook RNA sequencing of circulating tumor cells (CTCs) obtained from blood samples of women with metastatic estrogen receptor (ER)+ breast cancer, comparing cases with progression in bone versus visceral organs. Among the activated cellular pathways in CTCs from bone-predominant breast cancer is Androgen Receptor (AR) signaling. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16288 77 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86978/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343124
Series		Accession: GSE86978	ID: 200086978

2292. RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation [RNA-Seq]
(Submitter supplied) Cellular response to ionizing radiation involves activation of the p53-dependent pathways and activation of the atypical NF-?B pathway. Mechanisms of the crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Novel genes potentially (co)regulated by p53 and NF-?B were found using high-throughput genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). 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/GSE110nnn/GSE110762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434471
Series		Accession: GSE110762	ID: 200110762

2293. RNA-seq of GSK-J4 Treated Neuroblastoma Cell Lines
(Submitter supplied) High-risk neuroblastoma is often distinguished by amplification of MYCN and loss of differentiation potential with tumors refractory to retinoic acid differentiation based therapies. Here, we leverage high-throughput drug screening of epigenetic targeted therapies across a large and diverse tumor cell line panel to uncover the hypersensitivity of neuroblastoma cells to GSK-J4, a small molecule dual inhibitor of H3K27 demethylases UTX and JMJD3. more...
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/GSE110nnn/GSE110709/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA434379
Series		Accession: GSE110709	ID: 200110709

2294. Therapy-induced hypoxia contributes to AML drug-resistance through BMX Kinase upregulation
(Submitter supplied) Oncogenic addiction to FLT3 kinase signaling is a hallmark of FLT3-ITD+ acute myeloid leukemia (AML). While FLT3 inhibitors like sorafenib show initial therapeutic efficacy, resistance rapidly develops through mechanisms that are incompletely understood. Here, utilizing RNA-Seq based analysis of patient leukemic cells, we found significant up-regulation of the Tec-family kinase BMX during sorafenib resistance. 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/GSE104nnn/GSE104594/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413146
Series		Accession: GSE104594	ID: 200104594

2295. Transcriptome profiling of HepG2 cells upon treatment of the menin-MLL inhibitor MI-503 or DMSO
(Submitter supplied) Hepatocellular carcinoma (HCC) accounts for the majority of malignant liver tumors and results in many deaths each year, emphasizing the need for new therapies. The protein-protein interaction between menin and histone methyltransferase Mixed Lineage Leukemia 1 (MLL1) plays an important role in the development of HCC, implying that pharmacologic inhibition of this interaction could lead to new therapeutic strategy for the HCC patients. 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/GSE103nnn/GSE103327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401703
Series		Accession: GSE103327	ID: 200103327

2296. Chemoprevention with COX2 and EGFR inhibition in FAP patients: mRNA signatures of duodenal neoplasia
(Submitter supplied) RNA sequencing of duodenal polyps in FAP patients treated with plabebo or the drug combination, erlotinib + sulindac
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 69 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94919/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374861
Series		Accession: GSE94919	ID: 200094919

2297. Next Generation Sequencing  Analysis of ADHFE1 and vector control Transcriptomes in breast cancer cells
(Submitter supplied) Our study represents a detailed analysis of MCF10A and MCF7 transcriptomes, with biologic replicates, generated by RNA-seq technology
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/GSE80nnn/GSE80537/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319220
Series		Accession: GSE80537	ID: 200080537

2298. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer
(Submitter supplied) Breast cancer metastasis remains a deadly disease with poorly understood clonal evolution and the timing with which drivers are acquired. Here, we present the RNA sequencing data as the RSEM upper quantile normalized data.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 83 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110590/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA226742
Series		Accession: GSE110590	ID: 200110590

2299. Human iPS-derived astroglia from a stable neural precursor state; improved functionality compared to conventional astrocytic models
(Submitter supplied) Characterization of different astrocytes soruces was done using RNAseq including samples from human primary adult brain, astrocytoma, and hiPSC derived astrocytes including neural stem cell origin
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/GSE109nnn/GSE109001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429370
Series		Accession: GSE109001	ID: 200109001

2300. Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology
(Submitter supplied) Renin, a key component in the regulation of blood pressure in mammals, is produced by the rare and highly specialized juxtaglomerular (JG) cells of the kidney. Although these cells line the media of the glomerular afferent arterioles and share some characteristics with contractile cells, they are filled with lysosome-like organelles where renin is activated and stored for regulated secretion in response to physiological and pathophysiological stimuli. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57401/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA246396
Series		Accession: GSE57401	ID: 200057401

2301. Interferon Gamma mRNA Signature in Tumor Biopsies Predicts Outcomes in Patients with Non–Small-Cell Lung Carcinoma or Urothelial Cancer Treated with Durvalumab
(Submitter supplied) An unmet need in cancer treatment is identification of biomarkers of response to PD-1 or PD-L1 immune checkpoint inhibitors that predict therapeutic outcomes in patients with non–small-cell lung carcinoma (NSCLC) and urothelial cancer (UC). Expression of PD-L1 measured by immunohistochemistry has limited capacity for predicting outcomes of immune checkpoint therapy because expression of this biomarker does not correlate highly with treatment response. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 159 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110390/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433587
Series		Accession: GSE110390	ID: 200110390

2302. RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer
(Submitter supplied) Long non-coding RNA (lncRNA) have been implicated in human pathology, however, their roles in colorectal carcinogenesis has not been fully elucidated. In the current study, whole-transcriptome was analyzed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. 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/GSE104nnn/GSE104178/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA411984
Series		Accession: GSE104178	ID: 200104178

2303. Development of Novel Patient Derived Xenografts from Breast Cancer Brain Metastases
(Submitter supplied) Brain metastases are an increasing burden among breast cancer patients, particularly for those with HER2+ and triple negative (TN) subtypes. Mechanistic insight into the pathophysiology of brain metastases and preclinical validation of therapies has relied almost exclusively on intracardiac injection of brain-homing cells derived from highly aggressive TN MDA-MB-231 and HER2+ BT474 breast cancer cell lines. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 5 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104020/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407970
Series		Accession: GSE104020	ID: 200104020

2304. Transcriptome-wide analysis of the role of HTLV-1 Tax PBM in T-Cells from infected humanized-mice (hu-Mice)
(Submitter supplied) Human T-lymphotropic virus type 1 (HTLV-1) is associated with the development of Adult T-cell Leukemia, an aggressive CD4+ T-cells malignancy. Here, we have developed a new procedure to infect humanized mice with proviruses displaying specific mutations, such as one leading to the loss of the PDZ domain-binding motif (PBM) of Tax. In order to specifically analyze the in vivo role of the PBM of Tax, a comparative study of infected hu-mice was performed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 6 Samples
FTP download: GEO (BEDGRAPH, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102220/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397039
Series		Accession: GSE102220	ID: 200102220

2305. TrapSeq: An RNA Sequencing-based pipeline for the identification of genetrap insertions in mammalian cells
(Submitter supplied) Current pipelines used to map genetrap insertion sites are based on inverse- or splinkerette-PCR methods, which despite their efficacy are prone to artifacts and do not provide information on the impact of the genetrap on the expression of the targeted gene. We developed a new method, which we named TrapSeq, for the mapping of genetrap insertions based on paired-end RNA sequencing. By recognizing chimeric mRNAs containing genetrap sequences spliced to an endogenous exon, our method identifies insertions that lead to productive trapping.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99483/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388635
Series		Accession: GSE99483	ID: 200099483

2306. Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma
(Submitter supplied) APE1 was knocked down using siRNA in low passage patient-derived PDAC cells and the resulting cells, along with control cells were analysed using scRNA-seq to identify differentially expressed genes and pathways as a result of APE1 knock-down.
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/GSE99nnn/GSE99305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388083
Series		Accession: GSE99305	ID: 200099305

2307. RNAseq data from Mesenchymal stem cells treated with TCDD or 1-methyl tryptophan
(Submitter supplied) Whole genome RNA-sequencing identified Nrf2, MAPK12 and IL-1a as important downstream targets of 1MT. We further demonstrate 1a1 and 1b1 activation by 1MT in IDO+ MSC following interferon-γ (IFNγ) activation, suggestive that 1MT-driven AHR signaling is uncoupled from IDO catalytic function. These observations support a novel paradigm by which AHR-activating compounds like 1MT can be used in cancer immunotherapy to stimulate a pro-inflammatory response, activating the body’s immune system to infiltrate and eradicate tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375931
Series		Accession: GSE95072	ID: 200095072

2308. RNA-Seq of Glioblastoma stem-like cell (GSC) NSC11 with and without 2Gy irradiation.
(Submitter supplied) RNA-Seq analyses of GSC line NSC11 after 2Gy irradiation in the transcriptome and the translatome to evaluate radiation-induced changes in alternative splicing.
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/GSE94nnn/GSE94693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371832
Series		Accession: GSE94693	ID: 200094693

2309. ATF4 inhibition by p62 represses stromal metabolic reprogramming and tumorigenesis II
(Submitter supplied) Tumors often undergo stress and need to reprogram their metabolism to survive and grow under nutrient challenging conditions. The stroma could play a critical role in this process by providing nutrients or signals to support the epithelial compartment of the tumor. Autophagy has been shown to play key roles both in the stroma and in the epithelium. However, how autophagy adaptors, such as p62, participate in the mechanisms whereby the stroma supports tumor progression is not yet fully understood. 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/GSE94nnn/GSE94367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369512
Series		Accession: GSE94367	ID: 200094367

2310. Two functionally distinct human Pan3 isoforms regulate mRNA turnover across the transcriptome
(Submitter supplied) Human Pan3 protein has two functionally distinct isoforms required for proper decay of mRNA across the transcriptome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86549/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342171
Series		Accession: GSE86549	ID: 200086549

2311. GDF6-induced BMP signaling reawakens a neural crest identity in melanoma to prevent cell death and differentiation
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Danio rerio; Homo sapiens
Type:		Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 37 Samples
FTP download: GEO (PAIR, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83400/
Series		Accession: GSE83400	ID: 200083400

2312. Differential gene expression of human melanoma cells [RNA-seq]
(Submitter supplied) We report the gene expression comparison of human A375 melanoma cells with GDF6 and BMP pathway modulation. These comparisons were used to determine the gene signature regulated by GDF6.
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/GSE83nnn/GSE83342/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325657
Series		Accession: GSE83342	ID: 200083342

2313. Alternative splicing of differentiated myeloid cell transcripts after infection by Anaplasma phagocytophilum impacts a selective group of cellular programs
(Submitter supplied) Eukaryotic proteome diversity exceeds that encoded within individual genes, and results in part from alternative splicing events of pre-messenger RNA. The diversity of these splicing events can shape the outcome in development and differentiation of normal tissues, and is important in pathogenic circumstances such as cancer and some heritable conditions. A role for alternative splicing of eukaryotic genes in response to viral and intracellular bacterial infections has only recently been recognized, and plays an important role in providing fitness for microbial survival, while potentially enhancing pathogenicity. 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/GSE107770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421330
Series		Accession: GSE107770	ID: 200107770

2314. Analysis of gene expression in SKOV3 ovarian cancer cells after knockdown of the long non-coding RNA DNM3OS
(Submitter supplied) RNA-sequencing was performed to gain insight into the mechanism responsible for the mesenchymal-to-epithelial transition (MET) induced by loss of long non-coding RNA (lncRNA) DNM3OS in SKOV3 ovarian cancer cells. Following siRNA-mediated knockdown of DNM3OS or non-targeting control,  RNA-sequencing was performed. This high-throughput data revealed knockdown of DNM3OS down-regulated the expression of genes and pathways known to induce EMT in ovarian cancer.
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/GSE104nnn/GSE104295/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412256
Series		Accession: GSE104295	ID: 200104295

2315. RNA-Seq analysis of breast cancer cells after shikonin treatment
(Submitter supplied) We performed RNA-seq analysis using differnt breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231) after shikonin treatment. We reported that shikonin enhances the expression of DUSP-1 and DUSP-2. Shikonin induces apoptosis and decreases the phosphorylation of JNK1/2 through activationg DUSP-1 and DUSP2.
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/GSE100nnn/GSE100687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392672
Series		Accession: GSE100687	ID: 200100687

2316. Methylation of Transcription Factor YY2 Regulates its Transcriptional Activity and Cell Proliferation
(Submitter supplied) Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context specific manner compared to YY1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 4 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96877/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379974
Series		Accession: GSE96877	ID: 200096877

2317. A cell cycle-based functional screen to identify lncRNA-based cancer biomarkers
(Submitter supplied) We report S-phase cancer associated lncRNAs which were identified using nascent RNA capture assay in HeLa cells. Coupling high throughput RNA sequencing with clinical investigation across TCGA datasets we identified a number of lncRNAs that act as prognostic biomarkers for survival in different cancer types
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL16791 GPL18723 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92250/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357034
Series		Accession: GSE92250	ID: 200092250

2318. ERK potentiates transactivation and oncogenic function of ERG by phosphorylation induced dissociation of PRC2 complex
(Submitter supplied) ERK activates ERG-mediated prostate cancer specific gene expression program by phopshorylation induced dissociation of PRC2 complex
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86232/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340977
Series		Accession: GSE86232	ID: 200086232

2319. Integrated analysis of methylome and transcriptome of Esophageal Squamous Cell Carcinoma by using Next Generation Sequencing
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16558 4 Samples
FTP download: GEO (BED, BEDGRAPH, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71412/
Series		Accession: GSE71412	ID: 200071412

2320. Transcriptome Analysis of Esophageal Squamous Cell Carcinoma by using Next Generation Sequencing
(Submitter supplied) We obtained transcriptome profiling (SAGE-seq) of esophageal squamous cell carcinoma (ESCC) and normal tissue specimens by using next generation sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16558 2 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71411/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291311
Series		Accession: GSE71411	ID: 200071411

2321. Sequencing of matched pair samples (diagnosis and relapse) in human B-cell acute lymphoblastic leukemia cells (ALL)
(Submitter supplied) The experiment focused on how B-cells respond transcriptionally to drug treatment in acute lymphocytic leukemia (ALL). We obtained B-cell samples from a patient at diagnosis (LAX7) and after the development of resistance (LAX7R) following a standard 3-week chemotherapy regimen (vincristine, dexamethasone, L-asparaginase and doxorubicin). The resistance sample possessed a KRASG12V mutation not present at diagnosis. more...
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/GSE102301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397377
Series		Accession: GSE102301	ID: 200102301

2322. RNA-seq of MCF10A cells and CAF
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106508/
Series		Accession: GSE106508	ID: 200106508

2323. RNA-seq of cancer-associated fibroblasts (CAF) treated with PBS or extracellular vesicles (EV) from MCF10A or MDA-MB-231 cells
(Submitter supplied) To identify gene expression changes associated with treatment of EV that carry high levels of miR-105 (from MDA-MB-231 and MCF10A/miR-105 cells) in human breast tumor derived CAF, we analyzed RNA isolated from PBS- or EV-treated CAF.  Gene expression in CAF treated with EV from MDA-MB-231 or MCF10A/miR-105 cells was compared to cells treated with PBS or EV from MCF10A cells, both of which served as controls in this experiment.
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/GSE106nnn/GSE106503/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417064
Series		Accession: GSE106503	ID: 200106503

2324. Knockdown of FOXP1 promotes the development of lung adenocarcinoma
(Submitter supplied) Lung cancer is one of the most common cancers in the world, which accounts for about 27% of all cancer deaths. However, the mechanisms underlying the pathogenesis of lung cancer cells remain largely elusive. In this study, we examined the role of the Forkhead box protein P1 (FOXP1) in lung cancer development. Our Oncomine analysis shows that FOXP1 is downregulated in lung adenocarcinoma compared with normal lung tissue. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108500/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427471
Series		Accession: GSE108500	ID: 200108500

2325. Transcriptome analysis of OSKM- or RAS-induced senescent IMR90 fibroblasts treated with Rapamycin.
(Submitter supplied) Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. 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/GSE103nnn/GSE103938/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407729
Series		Accession: GSE103938	ID: 200103938

2326. The deregulated microRNAome contributes to the cellular response to aneuploidy
(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: GPL16791 60 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102855/
Series		Accession: GSE102855	ID: 200102855

2327. The deregulated microRNAome contributes to the cellular response to aneuploidy [mRNA]
(Submitter supplied) Aneuploidy severely alters cell physiology and is widespread in cancers and other pathologies. In model cell lines, aneuploidy impairs proliferation, leads to proteotoxic as well as replication stress and triggers conserved transcriptome and proteome changes. In this study we analysed for the first time miRNAs and demonstrate that their expression is altered in response to chromosome gain.
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/GSE102nnn/GSE102852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399124
Series		Accession: GSE102852	ID: 200102852

2328. Coupling shRNA screens with single-cell RNA-Seq identifies mechanisms regulating senescence during reprogramming
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1513 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95021/
Series		Accession: GSE95021	ID: 200095021

2329. Coupling shRNA screening with single-cell RNA-Seq identifies mechanisms regulating senescence during reprogramming
(Submitter supplied) Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 376 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95020/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375751
Series		Accession: GSE95020	ID: 200095020

2330. Single-cell RNA-Sequencing of IMR90 fibroblasts bypassing reprogramming-induced senescence
(Submitter supplied) Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 620 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94980/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375078
Series		Accession: GSE94980	ID: 200094980

2331. Single-cell RNA Sequencing as a tool for simultaneous shRNA detection and transcriptome analysis in the context of functional shRNA screens
(Submitter supplied) Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 460 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94979/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375079
Series		Accession: GSE94979	ID: 200094979

2332. Transcriptome analysis of IMR90 fibroblasts expressing OSKM or control vector and OSKM-induced senescent IMR90 fibroblasts upon p21CIP or mTOR knockdown
(Submitter supplied) Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. more...
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/GSE94nnn/GSE94928/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374859
Series		Accession: GSE94928	ID: 200094928

2333. Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes
(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 GPL18460 GPL9115 63 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110387/
Series		Accession: GSE110387	ID: 200110387

2334. Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes [RNA-seq]
(Submitter supplied) The NF-κB transcription factors are activated via diverse molecular mechanisms in response to various types of stimuli. A plethora of functions associated with specific sets of target genes could be regulated differentially by this factor, affecting cellular response to stress including an anticancer treatment. Here we aimed to compare subsets of NF-κB-dependent genes induced in cells stimulated with a pro-inflammatory cytokine and in cells damaged by a high dose of ionizing radiation (4 and 10 Gy). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 45 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110386/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433583
Series		Accession: GSE110386	ID: 200110386

2335. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function
(Submitter supplied) VCP is an evolutionary conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome pathway. Despite the central role of VCP in the regulation of protein homeostasis, identity and nature of its cellular substrates remain poorly defined. Here, we combined chemical inhibition of VCP and quantitative ubiquitin remnant profiling to assess the effect of VCP inhibition on the ubiquitin-modified proteome and to probe the substrate spectrum of VCP in human cells. 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/GSE107nnn/GSE107313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419745
Series		Accession: GSE107313	ID: 200107313

2336. USP15-dependent lysosomal pathway controls p53-R175H turnover in ovarian cancer cells
(Submitter supplied) Gain-of-function p53 mutants such as p53-R175H form stable aggregates that accumulate in cells and play an important role in cancer progression. Selective degradation of gain-of-function p53 mutants has emerged as a highly attractive therapeutic strategy to target cancer cells harboring specific p53 mutations. We identified a small molecule called MCB-613 to cause rapid ubiquitination, nuclear export, and degradation of p53-R175H through lysosome-mediated pathway leading to catastrophic cancer cell death. 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/GSE110nnn/GSE110220/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433198
Series		Accession: GSE110220	ID: 200110220

2337. Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1
(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 20 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107556/
Series		Accession: GSE107556	ID: 200107556

2338. Transcriptome analysis of SKI knock-out in HL60 cells
(Submitter supplied) Whole transcriptome for SKI knock-out and control HL60 cells was sequenced. SKI control and knockout samples were compared to find differentially expressed genes. Differentially expressed genes were further analysed to find the significance of SKI in HL60 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107555/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420737
Series		Accession: GSE107555	ID: 200107555

2339. Lung Cancer Cell-Mediated Skeletal Muscle Mitochondrial Dysfunction is Mitigated by 1a,25-Dihydroxyvitamin D3
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL21103 24 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103550/
Series		Accession: GSE103550	ID: 200103550

2340. Gene  expression profiles of ibrutinib-responsive and ibrutinib non-responsive cells in ERBB4 expressing cancer cell lines
(Submitter supplied) By  using a unique functional protein microarray platform, we found that the FDA approved drug ibrutinib can inhibits ERBB4 activity in the same nM range as its canonical target, BTK. Cell-based assays revealed that ibrutinib treatment inhibited cell growth in some ERBB4 expressing cancer cells whereas no response was observed in other cells. Therefore, to identify global gene expression differences between ibrutinib responsive and non-responsive cancer cells, we performed RNA-Seq, and identified a signature featuring the WNT pathway that predicts growth responsiveness to ibrutinib in ERBB4 expressing cancers.
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/GSE102nnn/GSE102744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398548
Series		Accession: GSE102744	ID: 200102744

2341. RNA-seq and ChIP-seq analysis of BMI1 or RING1B-silenced prostate cancer cells C4-2
(Submitter supplied) Purpose: Study of the role of BMI1 dependent and indpendent of PRC1 in castration-resistant prostate cancer(CRPC)   Method: The expression of BMI1 or RING1B was silenced by 2 independent siRNA strands targeted at BMI1 or RING1B in C4-2 cells, scramble RNA as control. mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing. AR, BMI1 and IgG ChIP was conducted in C4-2 cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382981
Series		Accession: GSE97831	ID: 200097831

2342. Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers
(Submitter supplied) Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69770/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA286733
Series		Accession: GSE69770	ID: 200069770

2343. Transcriptomic analysis of multiple myeloma cell lines
(Submitter supplied) We found that a small molecule inhibitor of PRMT4 inhibited cell growth of a subset of multiple myeloma cell lines. To identify biomarkers that predict the sensitivity of myeloma cells to PRMT4 inhibition, we performed transcriptomic analysis of multiple myeloma cell lines.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110180/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA433025
Series		Accession: GSE110180	ID: 200110180

2344. A practical evaluation of alignment algorithms for RNA variant calling analysis
(Submitter supplied) We performed RNA-seq with ten pieces of breast cancer (invasive ductal carcinoma; luminal B type) tissue and three pieces of adjacent normal tissue from a single patient. These RNA-seq data were used to evaluate the performance of splice-aware aligners.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110114/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432903
Series		Accession: GSE110114	ID: 200110114

2345. Luminal lncRNAs Regulation by ERα-controlled Enhancers in a Ligand-independent Manner in Breast Cancer Cells
(Submitter supplied) Estrogen receptor-α (ERα) is a ligand-inducible protein which mediates estrogenic hormones signaling and defines the luminal breast cancer phenotype. Recently, we demonstrated that ERα binds chromatin in absence of ligand (apoERα) regulating transcription of protein-coding genes and several lncRNAs. Noteworthy, apoERα-regulated lncRNAs marginally overlap estrogen-induced transcripts representing a signature of luminal breast cancer genes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108693/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428309
Series		Accession: GSE108693	ID: 200108693

2346. ZNF131 suppresses centrosome fragmentation in Glioblastoma stem-like cells through regulation of HAUS5
(Submitter supplied) To identify new Glioblastoma multiforme (GBM) therapeutic strategies, we previously performed genome-wide RNAi lethality screens in patient-derived GBM stem-like cells (GSCs) and neural progenitor cells (NPCs) to identify genes required for the self-renewal of GSC isolates, but which are dispensable for NPCs.  Here we report the retest of the GSC-lethal gene ZNF131, which encodes a novel vertebrate-specific BTB domain zinc finger transcription factor that is broadly required for GSC viability. 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/GSE95nnn/GSE95027/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375764
Series		Accession: GSE95027	ID: 200095027

2347. miR25/93 mediates the hypoxia-induced immunosuppression by repression of cGAS
(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
Platforms: GPL16791 GPL18573 6 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79789/
Series		Accession: GSE79789	ID: 200079789

2348. Total nucleoplasmic RNA-seq in MCF-7
(Submitter supplied) Deep sequencing of total RNA isolated from the nucleoplasmic fraction of MCF-7 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 1 Sample
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110149/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432953
Series		Accession: GSE110149	ID: 200110149

2349. Cross-Species Approach Identifies MELK as a Potential Therapeutic Target in Prostate Cancer
(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 GPL16791 120 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101539/
Series		Accession: GSE101539	ID: 200101539

2350. Identification of MELK-regulated genes in prostate cancer cells using next-generation sequencing
(Submitter supplied) A cross-species analysis identified MELK as a potential therapeutic target in prostate cancer. To further elucidate the functional role of MELK in prostate cancer cells, we aimed to identify MELK-regulated genes. C4-2b cells were either treated with a small-molecule MELK inhibitor (OTSSP167), or transfected with siRNAs targeting MELK. Differentially expressed genes were identified using next-generation sequencing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94570/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371482
Series		Accession: GSE94570	ID: 200094570

2351. RNA sequencing for transcriptome comparison between HTLV-1 Tax(-) and Tax(+) cells in Adult T-cell leukemia cell lines (MT-1 and KK-1)
(Submitter supplied) Initially, ATL cell lines (MT-1 or KK-1) were stably transfected  with reporter plasmid for HTLV-1 Tax expression, and single clones were isolated . This reporter in composed of Tax responsive element upstream of d2EGFP fluorescent protein. d2EGFP is expressed upon Tax expression in any individual cell. To compare transcriptomes of Tax(-) and Tax(+) cells, FACS sorting was done for d2EGFP(-) and d2EGFP(+) populations and RNA sequencing was performed.
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/GSE108nnn/GSE108601/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427802
Series		Accession: GSE108601	ID: 200108601

2352. Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer
(Submitter supplied) Male breast cancer (MBC) is rare and poorly characterized. Like the female counterpart, most MBCs are hormonally driven, but resistance to hormonal treatment is common. We use transcriptomics to reveal gender-selective and genomic location-specific hormone receptor actions, which associated with survival in MBC patients.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 46 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104730/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413693
Series		Accession: GSE104730	ID: 200104730

2353. HNRNPH1 is required for rhabdomyosarcoma cell growth and survival
(Submitter supplied) Rhabdomyosarcoma (RMS) is an aggressive and difficult to treat cancer characterized by a muscle-like phenotype. Although the average 5-year survival rate is 65% for newly diagnosed RMS, the treatment options for metastatic disease are limited in efficacy, with the 5-year survival rate plummeting to 30%. Heterogenous nuclear ribonucleoprotein H1 (HNRNPH1) is an RNA-binding protein that is highly expressed in many cancers, including RMS. more...
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/GSE104nnn/GSE104559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413052
Series		Accession: GSE104559	ID: 200104559

2354. RNA sequencing (RNA-SEQ) of PSPC1 knockdown by shRNA in A549 cells
(Submitter supplied) We show that PSPC1 is required for cancer cell motilities and stemness properties in vitro and lung metastasis in vivo. We used high throughput sequencing to analyze the PSPC1 regulated gene expression. Loss of PSPC1 results in significant gene expression level changes in thousands of individual transcripts in key regulators of the EMT, CSCs and TGFb signaling.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65523/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA274272
Series		Accession: GSE65523	ID: 200065523

2355. Antibody-Mediated Inhibition of MICA/B Shedding Promotes NK Cell-Driven Tumor Immunity
(Submitter supplied) MICA and MICB (MICA/B) are expressed by many human cancers due to cellular stress and tag cells for elimination by cytotoxic lymphocytes through NKG2D receptor activation.  However, tumors evade this immune recognition pathway through proteolytic shedding of MICA/B proteins.  We rationally designed antibodies targeting the MICA α3 domain, the site of proteolytic shedding, and found that these antibodies prevented loss of cell surface MICA/B by human cancer cells. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL18573 9 Samples
FTP download: GEO (CSV, MTX, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109542/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431361
Series		Accession: GSE109542	ID: 200109542

2356. Natural Killer cells control tumor growth by sensing a growth factor
(Submitter supplied) Many tumors produce platelet-derived growth factor (PDGF)-DD, which promotes cellular proliferation, epithelial-mesenchymal transition, stromal reaction, and angiogenesis through autocrine and paracrine PDGFRβ signaling. By screening a secretome library, we found that the human immunoreceptor NKp44 encoded by NCR2 and expressed on natural killer (NK) cells and innate lymphoid cells recognizes PDGF-DD. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 27 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107047/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418917
Series		Accession: GSE107047	ID: 200107047

2357. FOXF1 defines the core-regulatory circuitry in gastrointestinal stromal tumor (GIST)
(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 38 Samples
FTP download: GEO (BIGWIG, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106626/
Series		Accession: GSE106626	ID: 200106626

2358. A Brain Penetrant Mutant IDH1 Inhibitor Provides In Vivo Survival Benefit
(Submitter supplied) We profiled two IDH1 mutant glioma models, grown as intracranial xenografts, treated with an IDH1 inhbitor.  One model, BT424, was responsive to IDH1 inhibition by compound treatement and also displayed more transcriptional changes in response to treatment.  The other model, GB10, was not responsive to IDH1 inhibition and was transcriptionally quiet after treatment with compound.
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/GSE105nnn/GSE105447/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415191
Series		Accession: GSE105447	ID: 200105447

2359. Identification of an IL-1-induced gene expression pattern in AR+ PCa cells that mimics the molecular phenotype of AR- PCa cells
(Submitter supplied) In immunosurveillance, bone-derived immune cells infiltrate the tumor and secrete inflammatory cytokines to destroy cancer cells.  However, cancer cells have evolved mechanisms to usurp inflammatory cytokines to promote tumor progression.  In particular, the inflammatory cytokine, interleukin-1 (IL-1), is elevated in prostate cancer (PCa) patient tissue and serum and promotes PCa bone metastasis.  IL-1 also represses androgen receptor (AR) accumulation and activity in PCa cells, yet the cells remain viable; suggesting that IL-1 may also contribute to AR-targeted therapy resistance. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 18 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105088/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414614
Series		Accession: GSE105088	ID: 200105088

2360. Functional and genomic characterization of a xenograft model system for the study of metastasis in triple-negative breast cancer.
(Submitter supplied) To define the molecular regulators of metastasis of triple-negative breast cancer, we conducted a rigorous characterization of four isogenic populations of MDA-MB-231 human triple-negative breast cancer cells that display a range of intrinsic spontaneous metastatic capacities in immuno-deficient mice, from non-metastatic to highly metastatic to lung, liver, spleen and spine. PAT-Seq gene expression profiling of primary tumor cells identified the fibroblast growth factor homologous factor, FGF13, as a candidate metastatic virulence gene highly upregulated in aggressively metastatic MDA-MB-231HM tumors.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 20 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101745/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395339
Series		Accession: GSE101745	ID: 200101745

2361. Next generation sequencing analysis of potential target genes of lncRNA BLACAT2
(Submitter supplied) Next generation sequencing analysis was performed to identify potential target genes of lncRNA BLACAT2.  Purified total RNA (3 μg) was used to deplete ribosomal RNA with Ribo-Zero rRNA Removal Kits (MRZMB126,Epicentre). Poly(A)+ RNA was purified with oligo(dT) magnetic beads and fragmented into short sequences. The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions. 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/GSE101nnn/GSE101287/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393943
Series		Accession: GSE101287	ID: 200101287

2362. Alternative classification of glioblastoma based on BUB1B-inhibition sensitivity
(Submitter supplied) We created a computational framework with which to predict BUB1B-GLEBS sensitivity based on gene expression data from BUB1B-inhibition sensitive (BUB1BS) or resistant (BUB1BR) GBM stem cells (GSCs), astrocytes, and neural progenitors. Our classifier examines the expression of 838 genes comprising the BUB1BS signature. Applying this scheme to GBM patient tumor data stratified tumors into BUB1BS and BUB1BR subtypes, revealing that BUB1BS patients have a significantly worse prognosis regardless of their tumor's development subtype (i.e., classical, mesenchymal, neural, proneural). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94874/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374705
Series		Accession: GSE94874	ID: 200094874

2363. Genes and mechanisms regulated by androgens as possible contributors to the male excess observed in autism
(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 50 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86458/
Series		Accession: GSE86458	ID: 200086458

2364. Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer
(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 high throughput sequencing
Platform: GPL16791 50 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109955/
Series		Accession: GSE109955	ID: 200109955

2365. Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [RNA-seq]
(Submitter supplied) Transcriptome levels of matched patient-derived xenograft (PDX) in vitro-in vivo models.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109903/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432416
Series		Accession: GSE109903	ID: 200109903

2366. SILAC identifies LAD1 as an oncogenic filamin binder regulating actin dynamics in response to EGF and marking aggressive breast tumors
(Submitter supplied) Mutations mimicking growth factor-induced proliferation and motility characterize some aggressive subtypes of mammary tumors. To unravel novel players, we applied phosphoproteomics on untransformed mammary cells, which were pre-stimulated with the epidermal growth factor (EGF). This analysis identified ladinin-1 (LAD1), a hitherto poorly characterized protein, as a phosphor-effector of the EGF-to-ERK pathway. 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/GSE103nnn/GSE103531/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401815
Series		Accession: GSE103531	ID: 200103531

2367. Transcriptome-wide response to synthetic chromatin protein PcTF: Breast Cancer
(Submitter supplied) The goal of this study was to identify genes that become upregulated in response to a synthetic transcription factor, PcTF, in a panel of breast cancer model cell lines. PcTF contains a conserved H3K27me3-binding chromodomain expressed in-frame with an mCherry fluorescent tag and a VP64 activation domain. Therefore, we expected genes with H3K27me3-associated promoters to become upregulated upon PcTF expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 27 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103520/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401827
Series		Accession: GSE103520	ID: 200103520

2368. Respecifying human iPSC-derived blood cells into highly engraftable hematopoietic stem and progenitor cells with a single factor
(Submitter supplied) Purpose: We designed this study to evaluate the feasibility of using only one factor to respecify human induced pluripotent stem cells (iPSCs)-derived blood cells into long-term engraftable hematopoietic stem and progenitor cells (HSPCs).  We also parallelly compared iPSC-derived HSPCs (iHSPCs) with primary HSPCs under the same induction and transplantation condition in order to examine the functional equivalency between iHSPCs and bona fide HSPCs. 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/GSE103nnn/GSE103420/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401855
Series		Accession: GSE103420	ID: 200103420

2369. Mitotically associated long non-coding RNA, MANCR regulates cell cycle in triple negative breast cancer cells 
(Submitter supplied) Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that is difficult to treat as it is unresponsive to hormone-therapy; therefore, it is imperative to identify novel, targetable regulators of progression in TNBC. Long non-coding RNAs (lncRNAs) are important regulators in breast cancer and have great potential as therapeutic targets; however, little is known about how the majority of lncRNAs function within TNBC cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102155/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396880
Series		Accession: GSE102155	ID: 200102155

2370. Transcriptome analysis of BAP1 knockout and restoration
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 21 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97225/
Series		Accession: GSE97225	ID: 200097225

2371. mRNA expression profile of Lymphocytes by high-throuput sequencing
(Submitter supplied) The activation of CD4+ T helper (Th) cells is crucial for the induction of cytotoxic T lymphocyte (CTL) responses against malignancy. We reprogrammed a Th clone specific for chronic myelogenous leukemia (CML)-derived b3a2 peptide to pluripotency and re-differentiated the cells into T-lineage cells (iPS-T cells). Although iPS-T cells retained the same T-cell receptor (TCR) as the original Th clone, their gene expression patterns resembled those of group 1 innate lymphoid cells, and CD4 molecule, an essential co-receptor in TCR-mediated Th responses, was not expressed. 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/GSE94nnn/GSE94332/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369394
Series		Accession: GSE94332	ID: 200094332

2372. Cross species transcriptome analysis of osteosarcoma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 155 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87686/
Series		Accession: GSE87686	ID: 200087686

2373. Next-gen RNA sequencing of human osteosarcoma tumors
(Submitter supplied) Trascriptome analysis of osteosarcoma samples were performed
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 52 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345424
Series		Accession: GSE87624	ID: 200087624

2374. RNA-Sequencing experiment for effects of PKF115-584 treatment on four T-ALL cell lines (RPMI8402, HPB-ALL, Jurkat, CCRF-CEM).
(Submitter supplied) Notch activation is instrumental in the development of most T-cell acute lymphoblastic leukemia (T-ALL) cases, yet Notch mutations alone are not sufficient to recapitulate the full human disease in animal models. We here found that Notch1 activation at the fetal liver (FL) stage expanded the hematopoietic progenitor population and conferred it transplantable leukemic-initiating capacity. However, leukemogenesis and leukemic-initiating cell capacity induced by Notch1 was critically dependent on the levels of β-Catenin in both FL and adult bone marrow contexts. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69157/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284673
Series		Accession: GSE69157	ID: 200069157

2375. Telomerase-mediated Strategy for Overcoming Non-Small Cell Lung Cancer Targeted Therapy and Multi-drug Chemotherapy Resistance
(Submitter supplied) Standard and targeted therapies almost universally fail due to tumor heterogeneity/plasticity leading to intrinsic or acquired drug resistance. We used the telomerase substrate precursor 6-thio-2’-deoxyguanosine (6-thio-dG) to target telomerase-expressing targeted therapy and platin-doublet chemotherapy resistant cells. We observed that erlotinib, paclitaxel/carboplatin and gemcitabine/cisplatin resistant cells are sensitive to 6-thio-dG in xenograft, syngeneic immunocompetent and genetically engineered mouse models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 54 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109821/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431789
Series		Accession: GSE109821	ID: 200109821

2376. Comparative Transcriptomics of Triple Negative Breast Cancer Stem Cells and Differentiated Tumor Cells Identifies Teneurin-4 as a Potential Therapeutic Target
(Submitter supplied) BACKGROUND: Triple-negative breast cancer (TNBC) is insensitive to the most effective therapies for other breast cancers, including endocrine and Her2-directed therapies, thus the lack of specific treatments prompted us to search for new TNBC-associated molecules to be used as targets for cancer therapy. As patients with TNBC usually experience a quicker relapse and metastatic progression compared to other breast cancer subtypes, we hypothesized that cancer stem cells (CSC) could play a central role in TNBC. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109798/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA432055
Series		Accession: GSE109798	ID: 200109798

2377. Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [RNA-seq]
(Submitter supplied) In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor (TF) MYCN is the defining prognosticator of high-risk disease, occurs in one-third of neuroblastoma, and drastically reduces overall survival rates1,2. As a proto-oncogene, targeted MYCN overexpression in peripheral neural crest is sufficient to initiate disease in mouse models3. In MYCN amplified neuroblastoma, elevated expression of the factor is crucial to maintain tumor stemness4,5 and is associated with increased proliferation and aberrant cell cycle progression, as these tumors lack the ability to arrest in G1 in response to irradiation6-9. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 49 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80153/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318042
Series		Accession: GSE80153	ID: 200080153

2378. On the design of CRISPR-based single cell molecular screens
(Submitter supplied) We demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 13 Samples
FTP download: GEO (MTX, RDS, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108699/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428344
Series		Accession: GSE108699	ID: 200108699

2379. Specific labeling of stem cell activity in human colorectal organoids using an ASCL2-responsive minigene
(Submitter supplied) Organoid technology provides the possibility to culture human colon tissue and patient-derived colorectal cancers (CRC) while maintaining all functional and phenotypic characteristics. Labeling of human colon stem cells (CoSCs), especially in normal and benign tumor organoids, is challenging and therefore limits usability of multi-patient organoid libraries for CoSC research. Here, we developed STAR (STem cell Ascl2 Reporter), a minimal enhancer/promoter element that reports transcriptional activity of ASCL2, a master regulator of LGR5+ CoSC fate. 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/GSE99nnn/GSE99133/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387402
Series		Accession: GSE99133	ID: 200099133

2380. Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma
(Submitter supplied) Amplification of the locus encoding the oncogenic transcription factor MYCN is a defining feature of high-risk neuroblastoma. Here we present the first dynamic chromatin and transcriptional landscape of MYCN perturbation in neuroblastoma. At oncogenic levels, MYCN associates with E-box binding motifs in an affinity-dependent manner, binding to strong canonical E-boxes at promoters and invading abundant weaker non-canonical E-boxes clustered at enhancers. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing
4 related Platforms 144 Samples
FTP download: GEO (BEDGRAPH, CEL, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80154/
Series		Accession: GSE80154	ID: 200080154

2381. HOXA9 cooperates with activated JAK/STAT signaling to drive leukemia development
(Submitter supplied) Leukemia is caused by the accumulation of multiple genomic lesions in hematopoietic precursor cells. However, how these events cooperate during oncogenic transformation remains poorly understood. We studied the cooperation between activated JAK3/STAT5 signaling and HOXA9 overexpression, two events identified as significantly co-occuring in T-cell acute lymphoblastic leukemia. Expression of mutant JAK3 and HOXA9 led to a rapid development of leukemia originating from multipotent or lymphoid-committed progenitors, with a significant decrease in disease latency compared to JAK3 or HOXA9 alone. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 32 Samples
FTP download: GEO (BEDGRAPH, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109653/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431601
Series		Accession: GSE109653	ID: 200109653

2382. Investigate A2M treatment on human prostate cancer and mouse liver
(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 GPL16791 22 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107195/
Series		Accession: GSE107195	ID: 200107195

2383. Investigate A2M treatment on human prostate cancer xenograft in mice
(Submitter supplied) Cancer resistance is a major cause for longevity of the naked mole-rat. Recent liver transcriptome analysis in this animal compared to wild-derived mice revealed higher expression of alpha2-macroglobulin (A2M) and cell adhesion molecules, which contribute to the naked mole-rat’s cancer resistance. Notably, A2M is known to dramatically decrease with age in humans. We hypothesize that this might facilitate tumor development. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106989/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418738
Series		Accession: GSE106989	ID: 200106989

2384. Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency [RNA-Seq]
(Submitter supplied) Recently, we reported that bacterial incorporation induces cellular transdifferentiation of human fibroblasts. However, the bacterium-intrinsic cellular- transdifferentiation factor remained unknown. Here, we found that cellular transdifferentiation is caused by ribosomes. Ribosomes, isolated from both prokaryotic and eukaryotic cells, induce the formation of embryoid body-like cell clusters. Numerous ribosomes are incorporated into both the cytoplasm and nucleus through trypsin-activated endocytosis, which leads to cell-cluster formation. 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/GSE99nnn/GSE99088/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387275
Series		Accession: GSE99088	ID: 200099088

2385. RNA-seq analysis of HuH-7, NCI-H1299 and HEK-293T cells
(Submitter supplied) The diversity and complexity of the cancer transcriptome hold the potential to yield tumor-specific transcripts (TSTs) in cancer. We report a novel LIN28B variant, LIN28B-TST, which is specifically expressed in hepatocellular carcinoma (HCC) and many other cancer types. LIN28B-TST initiates from a de novo alternative transcription initiation site. We found that LIN28B-TST was expressed in HuH-7 HCC cells and NCI-H1299 lung cancer cells, while wild-type LIN28B (LIN28B-WT) was expressed in HEK-293T human embryo kidney cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 3 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109528/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431305
Series		Accession: GSE109528	ID: 200109528

2386. Functional modulation of gene expression by TUC338 during growth of human
(Submitter supplied) In this study, we have investigated the molecular interactions of an ultraconserved non-coding RNA, TUC338, which is highly upregulated in hepatocellular cancer and implicated in growth regulation. We have identified functional genomic and proteomic determinants of this lncRNA involved in modulation of gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platform: GPL15520 2 Samples
FTP download: GEO (FA) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109490/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431205
Series		Accession: GSE109490	ID: 200109490

2387. Next-generation RNA-sequencing data of models of Ewing sarcoma with modulated expression of the lncRNA HOTAIR
(Submitter supplied) Purpose: Our experimental results demonstrate an essential role for the lncRNA HOTAIR in Ewing sarcoma. We have repressed HOTAIR expression in three Ewing sarcoma cell lines and overexpressed HOTAIR, alone and with EWS-FLI1, in htert-immortalized human mesenchymal stem cells to evaluate its effects on gene expression in this cancer. Methods: RNA-Seq of Ewing sarcoma cell lines with HOTAIR represssed by GapmeR or treated with nonsilencing control, and hTERT-immortalized hMSCs with expression of control GFP, HOTAIR, or HOTAIR and EWS-FLI1, was used for gene expression analysis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 40 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109483/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA431175
Series		Accession: GSE109483	ID: 200109483

2388. Gene induction by the USP6 oncogene in response to interferon
(Submitter supplied) We examined the role of the USP6 oncogene in the patient-derived immortalized ewing sarcoma cell line RD-ES. RNA-sequncing revealed that USP6 induces numerous genes that overlap with genes induced by interferon treatment. When USP6-expressing cells were treated with IFN, many of the overlapping genes were synergistically upregulated, indicating an overlap in signaling pathways.
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/GSE107nnn/GSE107307/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419740
Series		Accession: GSE107307	ID: 200107307

2389. Analysis of transcriptional regulation by Myt1 and Myt1l
(Submitter supplied) We report the changes in gene expression in U87 glioblastoma cells with re-introduced Myt1 or Myt1l.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103790/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407054
Series		Accession: GSE103790	ID: 200103790

2390. Targeting KRAS mutant cancers with a covalent G12C-specific inhibitor
(Submitter supplied) We report RNAseq gene expression data following ARS-1620 treatment and shKRAS expressing cells (NCI-H358).  We also compare gene expression changes following treatment with ARS-1620 or trametinib in NCI-H358, LU65 (KRAS-G12C+), and A549 (KRAS-G12S+) cells.  Additionally we report a time course (4, 24, 48hr) of ARS-1620 and trametinib treated NCI-H358 cells.
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/GSE103nnn/GSE103021/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399830
Series		Accession: GSE103021	ID: 200103021

2391. ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream of transcription start sites at the majority of CpG island promoters
(Submitter supplied) We performed ChIP-seq in four cancer cell lines to identify ZFX binding sites throughout the human genome. We also performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucelosome, suggesting that ZFX may play a critical role in promoter architecture. 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
Platforms: GPL21290 GPL20301 GPL11154 47 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102616/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398222
Series		Accession: GSE102616	ID: 200102616

2392. Transcriptome profiling of A2M treated A549 Cell Line Samples
(Submitter supplied) The goal of the study was to identify changes in transcriptome expressions upon treatment of A549 cell line samples with activated A2M.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 11 Samples
FTP download: GEO (GTF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106261/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416066
Series		Accession: GSE106261	ID: 200106261

2393. Targeting multiple effector pathways in pancreatic ductal adenocarcinoma with a G-quadruplex-binding small molecule
(Submitter supplied) Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signalling pathways. A novel approach to the treatment of PDAC is described, involving the targeting of cancer genes in PDAC pathways having over-representation of G-quadruplexes, using the quadruplex-binding compound CM03. This has been designed by computer modelling, is a potent inhibitor of cell growth in PDAC cell lines and has anti-cancer activity in PDAC models, with a superior profile compared to gemcitabine, a commonly used therapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 104 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105083/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414612
Series		Accession: GSE105083	ID: 200105083

2394. Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia
(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: GPL16791 71 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95656/
Series		Accession: GSE95656	ID: 200095656

2395. Coding and noncoding transcriptome sequencing of KRAS mutated colorectal tumors and adjacent tissues from cancer patients and KRAS mutated Aberrant Crypt Foci and matching normal crypts from healthy individuals [RNA-Seq]
(Submitter supplied) Colorectal cancer (CRC) is characterized by genome-wide alterations to DNA methylation that influence gene expression and genomic stability. Less is known about the extent to which methylation is disrupted in the earliest stages of CRC development. In this study we have combined laser-capture microdissection (LCM) with reduced representation bisulfite sequencing (RRBS) to identify cancer associated DNA methylation changes in human aberrant crypt foci (ACF), the earliest putative precursor to CRC. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 31 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95132/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376161
Series		Accession: GSE95132	ID: 200095132

2396. Che-1 is targeted by c-Myc to sustain proliferation in pre-B-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: GPL18573 31 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93628/
Series		Accession: GSE93628	ID: 200093628

2397. Che-1 is targeted by c-Myc to sustain proliferation in pre-B-cell acute lymphoblastic leukemia [RNA-seq]
(Submitter supplied) This Series contain trascriptional profiling via RNA-seq for two ALL-B cell lines, one commercial (NALM-6), one patient-derived (LAL-B), in presence or absence of AATF transcript. In NALM-6, also MYC was depleted and sequenced in triplicate. Furthermore, the Burkitt's Lymphoma P493 cell line has been sequenced in presence or absence of Tetracycline (MYC On-Off) and in CN vs siAATF.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 27 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93627/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361308
Series		Accession: GSE93627	ID: 200093627

2398. Molecular portraits of tumor mutational and micro-environmental sculpting by immune checkpoint blockade therapy
(Submitter supplied) Immune checkpoint blockade (ICB) has demonstrated significant promise for the treatment of advanced malignancies. Anti-CTLA4 and ant-PD1 therapy can activate the immune system and result in durable control in diseases such as melanoma and non-small cell lung cancer.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 109 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91061/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356761
Series		Accession: GSE91061	ID: 200091061

2399. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF
(Submitter supplied) It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex forming capacity promote exon inclusion. Destroying G-quadruplex forming capacity while keeping G-tracts intact abrogates exon inclusion. 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/GSE107nnn/GSE107542/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420499
Series		Accession: GSE107542	ID: 200107542

2400. Aberrant mRNA m6A methylation promotes the progression of endometrial cancer by altering Akt activity
(Submitter supplied) The N6-methyladenosine (m6A) methylation of mRNA is an emerging gene regulatory mechanism that controls the stability and translation of methylated transcripts in development and cell differentiation. Here, we show that aberrant m6A methylation plays key roles in the progression of endometrial cancer. About 70% of endometrial tumors exhibit reduced m6A methylation due to either mutation in METTL14 (~10%) or decreased expression of METTL3 (~60%). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 32 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93911/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362818
Series		Accession: GSE93911	ID: 200093911

2401. A toxicogenomics approach to screen chlorinated flame retardants tris(2-chloroethyl) phosphate and tris(2-chloroisopropyl) phosphate for potential health effects
(Submitter supplied) Tris(2-chloroethyl) phosphate (TCEP) is a pervasive flame retardant that has been identified as a chemical of concern given its health effects and therefore its use has since been tightly regulated. Tris(2-chloroisopropyl) phosphate (TCIPP), an analogue of TCEP, is believed to be its replacement. However, compared to TCEP, little is known of the toxicological impacts of TCIPP. We used RNA sequencing as unbiased and sensitive tool to identify and compare effects on a transcriptome level of TCEP and TCIPP in the human hepatocellular carcinoma cell line, HepG2. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430954
Series		Accession: GSE109463	ID: 200109463

2402. The translation termination factor GSPT1 is a phenotypically relevant off-target of heterobifunctional phthalimide degraders
(Submitter supplied) Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase cereblon (CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. 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/GSE108nnn/GSE108763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428512
Series		Accession: GSE108763	ID: 200108763

2403. RNA seq of pancreatic cancer-associated fibroblasts
(Submitter supplied) Transcriptomic profiling of pancreatic cancer-associated fibroblasts (CAFs) was done to evaluate the expression of GPCRs. The same was also done for normal pancreatic stellate cells, so as to evaluate whether a population of GPCRs shows increased expression in CAFs vs their normal precursors. We report the discovery of a novel GPCR in CAFs; we demonstrate this GPCR helps to drive the cross-talk between CAFs and cancer cells, enhancing the growth of pancreatic cancer cells.
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/GSE101665/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395149
Series		Accession: GSE101665	ID: 200101665

2404. Mutant p53 controls tumor metabolism and metastasis by regulating PGC-1α
(Submitter supplied) Mutant forms of p53 protein often possess pro-tumorigenic function, conferring increased survival and migration to tumor cells via its “gain of function” activity.  Whether and how a common polymorphism in TP53 at amino acid 72 (Pro72Arg, hereafter P72 and R72) impacts this gain of function has not been determined.  We show that mutant p53 enhances migration and metastasis of tumors through the ability to bind and regulate PGC-1α, and that this regulation is markedly impacted by the codon 72 polymorphism. 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/GSE109nnn/GSE109373/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA430702
Series		Accession: GSE109373	ID: 200109373

2405. AICDA-induced epigenetic plasticity accelerates germinal center-derived lymphomagenesis
(Submitter supplied) Epigenetic heterogeneity is emerging as a significant phenotypic feature of tumors. In diffuse large B-cell lymphomas (DLBCLs), increased cytosine methylation heterogeneity is associated with poor clinical outcome, yet the biological mechanisms driving epigenetic heterogeneity remain unclear. Activation-induced cytidine deaminase (AICDA), an enzyme that deaminates and facilitates demethylation of DNA methyl-cytosines in germinal center (GC) B-cells, is required for DLBCL pathogenesis and linked to inferior clinical outcomes. more...
Organism:	Homo sapiens; Mus musculus
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platforms: GPL11154 GPL17021 GPL13112 88 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375214
Series		Accession: GSE95013	ID: 200095013

2406. RNA-Seq of Kaposi’s sarcoma reveal alterations in glucose and lipid metabolism
(Submitter supplied) Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma (KS). In sub-Saharan Africa, the high prevalence of both HIV-1 and KSHV has made KS a leading cancer in the region, associated with poor prognosis and high mortality due to late medical presentation and advanced disease stages. A better understanding of the cellular and viral transcriptome profiles during neoplastic growth will aid in the definition of biomarkers and cellular functions associated with KS tumorigenesis and progression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100684/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392660
Series		Accession: GSE100684	ID: 200100684

2407. Transcription factors operate across disease loci: EBNA2 in autoimmunity
(Submitter supplied) Explaining the genetics of many diseases is challenging because most associations localize to regulatory regions. We present a novel computational method for discovering disease-driving mechanisms acting across multiple disease-associated, non-coding genomic regions. Application to a matrix of 213 phenotypes and 1,544 transcription factor (TF) binding datasets identifies 2,264 significant associations for hundreds of TFs in 92 phenotypes, including prostate and breast cancers. more...
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/GSE93nnn/GSE93709/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362187
Series		Accession: GSE93709	ID: 200093709

2408. Chromosomal instability promotes metastasis through a cytosolic DNA response
(Submitter supplied) Chromosomal instability (CIN) is a hallmark of cancer, and it results from ongoing errors in chromosome segregation during mitosis. While CIN is a major driver of tumor evolution, its role in metastasis has not been established. Here we show that CIN promotes metastasis by sustaining a tumor-cell autonomous inflammatory response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose envelopes frequently rupture exposing their DNA content to the cytosol. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 51 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384217
Series		Accession: GSE98183	ID: 200098183

2409. Isolation and Functional Interrogation of Adult Human Prostate Epithelial Stem Cells at Single Cell Resolution
(Submitter supplied) Using primary cultures of normal human prostate epithelial cells, we developed a novel prostasphere-based, label-retention assay that permits identification and isolation of stem cells at a single cell level. Their bona fide stem cell nature was confirmed using in vitro and in vivo regenerative assays and documentation of symmetric/asymmetric division. Robust WNT10B and KRT13 expression without E-cadherin or KRT14 staining distinguished individual stem cells from daughter progenitors in spheroids. 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/GSE95nnn/GSE95542/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377407
Series		Accession: GSE95542	ID: 200095542

2410. Positively selected enhancer elements endow tumor cells with metastatic competence
(Submitter supplied) Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in signature enhancer-histone marks between near-isogenic pairs of high and low lung-metastatic osteosarcoma cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 91 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299597
Series		Accession: GSE74230	ID: 200074230

2411. Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq.
(Submitter supplied) Tris (2-butoxyethyl) phosphate (TBOEP) is a compound produced at high volume that is used as both a flame retardant and a plasticizer. It is persistent and bioaccumulative, yet little is known of its toxicological modes of action. Such insight may aid risk assessment in a weight-of-evidence approach supplementing current testing strategies. We used an RNA sequencing approach as an unbiased and sensitive tool to explore potential negative health effects of sub-cytotoxic concentrations of TBOEP on the transcriptome of the human liver hepatocellular carcinoma cell line, HepG2, with the lowest concentration used potentially holding relevance to human physiological levels. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429571
Series		Accession: GSE109072	ID: 200109072

2412. Triplet nucleotide repeat-based siRNAs are highly toxic to cancer cells
(Submitter supplied) Triplet repeat siRNAs as found amplified in diseases such as Huntingtons disease can be used to kill cancer cells
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/GSE104nnn/GSE104552/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413038
Series		Accession: GSE104552	ID: 200104552

2413. Targeted inhibition of STAT/TET1 axis as a potent therapeutic strategy for acute myeloid leukemia
(Submitter supplied) Effective therapy of acute myeloid leukemia (AML) remains an unmet need. DNA methylcytosine dioxygenase Ten-eleven translocation 1 (TET1) is a critical oncoprotein in AML. Through a series of data analysis and drug screening, we identified two compounds (i.e., NSC-311068 and NSC-370284) that selectively suppress TET1 transcription and 5-hydroxymethylcytosine (5hmC) modification, and effectively inhibit cell viability in AML with high level expression of TET1 (i.e., TET1-high AML), including AML carrying t(11q23)/MLL-rearrangements and t(8;21) AML. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101480/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394528
Series		Accession: GSE101480	ID: 200101480

2414. Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines
(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 27 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100076/
Series		Accession: GSE100076	ID: 200100076

2415. Discovery of naturally occurring ESR1 mutations during acquisition of resistance to endocrine therapy in widely used estrogen receptor positive breast cancer cell lines [RNA-Seq]
(Submitter supplied) We report the first discovery of naturally occurring ESR1Y537C and ESR1Y537S mutations in MCF7 and SUM44 ESR1-positive cell-lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100075/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390636
Series		Accession: GSE100075	ID: 200100075

2416. Oncogenic roles of ARID5B in T-ALL
(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: GPL20301 21 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97514/
Series		Accession: GSE97514	ID: 200097514

2417. Integrative proteogenomic characterization of colorectal cancer cell lines and primary tumors
(Submitter supplied) Integrative analysis of global RNASeq and proteomic data comparing human colorectal cancer (CRC) cell lines to primary tumors and normal tissues.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90830/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356065
Series		Accession: GSE90830	ID: 200090830

2418. Mechanisms of tolerance and resistance to EGFR inhibition in lung cancer [RNA-seq]
(Submitter supplied) Purpose: Multiple mechanims have been proposed that lead to reduced effectiveness of EGFR tyrosine kinase inhibitors (TKIs) in lung cancer and yet resistance to osimertinib and gefitinib still remains a challenge in the clinic. The goals of this study are to identify key genes contributing to tolerance and resistance to EGFR inhibition. Methods: mRNA profiles of gefitinib and osimertinib tolerant cells in PC9 and HCC827 cells were generated by deep sequencing using Illumina. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 21 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103350/
Series		Accession: GSE103350	ID: 200103350

2419. RNA-sequencing in A549 cells transfected with TUFT1 siRNA
(Submitter supplied) We searched for roles of TUFT1 by RNA-seq in lung cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99149/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387432
Series		Accession: GSE99149	ID: 200099149

2420. 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 (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109028/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429446
Series		Accession: GSE109028	ID: 200109028

2421. A cytoplasmic COMPASS is necessary for cell survival and triple-negative breast cancer pathogenesis by regulating metabolism
(Submitter supplied) Mutations and translocations within the COMPASS (complex of proteins associated with Set1) family of histone lysine methyltransferases are associated with a large number of human diseases, including cancer. Here we report that SET1B/COMPASS, which is essential for cell survival, surprisingly has a cytoplasmic variant. SET1B, but not its SET domain, is critical for maintaining cell viability, indicating a novel catalytic-independent role of SET1B/COMPASS. 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 (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86855/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342781
Series		Accession: GSE86855	ID: 200086855

2422. Role of SUMOylation in differential ERα transcriptional repression by SERMs and pure antiestrogens in breast cancer cells
(Submitter supplied) RNA-seq: Gene expression profiling in MCF-7 cells treated with vehicle (0), estradiol (E2), the Selective ER Modulator 4-hydroxytamoxifen (OHT), or the pure antiestrogen fulvestrant (ICI). ChIP-seq: Genome-wide DNA binding profile of ERα and SUMO2/3 in MCF-7 cells treated with vehicle, E2 or ICI.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 40 Samples
FTP download: GEO (TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108883/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA429003
Series		Accession: GSE108883	ID: 200108883

2423. A cell-permeable stapled peptide inhibitor of the estrogen receptor/coactivator interaction
(Submitter supplied) We and others have proposed that coactivator binding inhibitors, which block the interaction of estrogen receptor and steroid receptor coactivators, may represent a potential class of new breast cancer therapeutics. The development of coactivator binding inhibitors has been limited, however, because many of the current molecules which are active in in vitro and biochemical assays are not active in cell-based assays. 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/GSE108nnn/GSE108308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423076
Series		Accession: GSE108308	ID: 200108308

2424. Transcriptome analysis of HGC-27 after infection with Sendai virus
(Submitter supplied) To better understand the interactions between Hippo signaling and antiviral signaling at transcription level, a high-throughput RNA-seq technology was utilized in gastric cancer cells HGC-27  at 48 hours after Sendai virus (SeV) infection.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107096/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418982
Series		Accession: GSE107096	ID: 200107096

2425. Abnormal RNA splicing and genomic instability after induction of DNMT3A mutations by CRISPR/Cas9 gene editing [RNA-Seq]
(Submitter supplied) Purpose: DNA methyltransferase 3A (DNMT3A) mediates de novo DNA methylation. Mutations in DNMT3A are associated with hematological malignancies, most frequently acute myeloid leukemia. DNMT3A mutations are hypothesized to establish a pre-leukemic state, rendering cells vulnerable to secondary oncogenic mutations and malignant transformation. However, the mechanisms by which DNMT3A mutations contribute to leukemogenesis are not well-defined. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (CSV, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96634/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379278
Series		Accession: GSE96634	ID: 200096634

2426. A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 36 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104309/
Series		Accession: GSE104309	ID: 200104309

2427. A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (RNA-seq)
(Submitter supplied) Targeting of general coactivators, such as BRD4, is an emerging strategy to interfere with oncogenic transcription factors (TFs) in cancer. However, coactivator perturbations have the potential to influence the function of numerous TFs, thereby resulting in biological pleiotropy. Here we identify TAF12, an 18 kilodalton subunit of TFIID/SAGA coactivator complexes, as a selective requirement for acute myeloid leukemia (AML) progression. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104308/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412430
Series		Accession: GSE104308	ID: 200104308

2428. Targeting the vulnerability of RB tumor suppressor loss in triple negative breast cancer
(Submitter supplied) Approximately 30% of TNBCs exhibit loss of function of the RB tumor suppressor. The study used RNA sequencing to profile RB-proficient and RB-deficient TNBC cases that were defined based on immunostaining for RB and p16ink4a.   The analyses revealed that RB-deficient TNBC cases express elevated levels of DNA replication and mitotic genes that could serve as the basis for increased sensitivity to drugs targeting cell cycle checkpoints.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL13393 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108757/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA428502
Series		Accession: GSE108757	ID: 200108757

2429. Intracranial aneurysm associated single-nucleotide polymorphisms alter regulatory DNA in the human circle of Willis
(Submitter supplied) Background and Purpose: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in six genomic loci. To gain insight into the relevance of these IA associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop. Methods: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in post mortem specimens of the human CoW. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL11154 14 Samples
FTP download: GEO (BED, TDF, TXT, XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107196/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419258
Series		Accession: GSE107196	ID: 200107196

2430. LNCaP treated with iBET
(Submitter supplied) BRD4 belongs to the bromodomain and extraterminal (BET) family of epigenetic reader proteins that bind acetylated histones and regulate gene expression. Pharmacological inhibition of BRD4 by BET inhibitors (BETi) has indicated antitumor activity against multiple cancer types. We define a new function for BRD4 that is distinct from its established role in transcriptional gene regulation. We show that BRD4 is essential for the repair of DNA double-strand breaks (DSBs), and mediates the formation of oncogenic gene rearrangements by engaging the non-homologous end joining (NHEJ) pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103907/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA408077
Series		Accession: GSE103907	ID: 200103907

2431. Study target genes of STAT3
(Submitter supplied) This study is to identify downstream genes regulated by STAT3 in response cytosolic acidification. Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment, cancer cells maintain alkaline intracellular pH (≥7.4) that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration and invasion. Here, we identify signal transducer and activator of transcription 3 (STAT3) as a key player in the maintenance of alkaline cytosolic pH. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108495/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427438
Series		Accession: GSE108495	ID: 200108495

2432. The E3 ubiquitin ligase HectD1 suppresses EMT and metastasis by targeting the +TIP protein ACF7 for degradation
(Submitter supplied) Cancer cells exploit the epithelial-to-mesenchymal transition (EMT) program toward metastasis. Cytoskeletal regulators are dually required in mesenchymal cells by promoting EMT-induced migration and sustaining the EMT program itself. In search for novel regulators of metastasis, we conducted an shRNA screen targeting a class of microtubule regulators, the plus-end tracking proteins (+TIPs). We show that the +TIP ACF7 is required for both the maintenance of EMT and to promote migration. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 8 Samples
FTP download: GEO (DIFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390660
Series		Accession: GSE100092	ID: 200100092

2433. Transcriptome sequencing (RNA-Seq) of non-tumor kidney tissues from 36 patients undergoing nephrectomy for exploring the metabolic mechanism of sorafenib and identifying the major transcriptional regulation factors in sorafenib metabolism in kidney
(Submitter supplied) The multi-kinase inhibitor drug sorafenib is used as first line treatment for hepatocellular carcinoma and advanced renal cell carcinoma. Sorafenib mainly undergos cytochrome P450 (CYP) 3A4-mediated oxidation and uridine diphosphate glucuronosyl transferase (UGT) 1A9-mediated glucuronidation in liver, but the biotransformation of sorafenib in kidney remains unclear. Therefore, we integrated the mRNA expression data of 36 kidney samples and the corresponding metabolic activities for sorafenib to study the metabolic mechanism of sorafenib in kidney.
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/GSE93nnn/GSE93069/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359795
Series		Accession: GSE93069	ID: 200093069

2434. Genome-wide analysis of STAT3 in diffuse large B-cell lymphoma
(Submitter supplied) By genome-wide ChIP-seq analysis in ABC DLBCL cell lines, we identified 2,251 STAT3 direct target genes, which involve B cell activation, survival, proliferation, differentiation and migration. Whole transcriptome profiling revealed that STAT3 acts as both a transcriptional activator and suppressor.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106844/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418173
Series		Accession: GSE106844	ID: 200106844

2435. Targeted RNA-Seq of Human Lymphoma Cell Line
(Submitter supplied) Thirty-seven (37) human cell lines were submitted to HTG Molecular for analysis using the HTG EdgeSeq Oncology Biomarker Panel. The goal of this work is to characterize the gene expression pattern of different cell lines bearing sensitivity or resistance for specific drugs.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103934/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407679
Series		Accession: GSE103934	ID: 200103934

2436. Genome-wide H3K4me3 and gene expression before and after methionine restriction in human cancer cells and mouse liver
(Submitter supplied) In this study, we compared genomic H3K4me3 and gene expression profiles before and after methionine restriction in human cancer cells and mouse liver. The goals are to understand the influences of nutrient availability on genomic architecture of histone modification and gene expression.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms 28 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA402050
Series		Accession: GSE103602	ID: 200103602

2437. Transcriptome of melanoma cell lines resistant to inhibition of the MAPK pathway.
(Submitter supplied) ABSTRACT: Despite major advances in targeted melanoma therapies, drug resistance limits their efficacy. Long noncoding RNAs (lncRNAs) are transcriptome elements that do not encode proteins but are important regulatory molecules. LncRNAs have been implemented in cancer development and response to different therapeutics and are thus potential treatment targets; however, the majority of their functions and molecular interactions remain unexplored. 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/GSE99nnn/GSE99867/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389808
Series		Accession: GSE99867	ID: 200099867

2438. Transcriptomic analysis of the HOTAIR-regulated genes
(Submitter supplied) An integrated RNA sequencing transcriptomic and quantitative proteomic analysis were employed to systematically explore the regulatory role of HOTAIR in HCC. A total of 673 transcripts and 298 proteins were identified to be dysregulated after HOTAIR inhibition.
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/GSE98nnn/GSE98091/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383988
Series		Accession: GSE98091	ID: 200098091

2439. Gene expression profile of CRC-derived HILEC
(Submitter supplied) HILEC from CRC tissues isolated from human patients underwent RNA sequencing to define their expression profile by comparison with healthy cells.
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/GSE93nnn/GSE93904/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362789
Series		Accession: GSE93904	ID: 200093904

2440. Basal-A Triple Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival
(Submitter supplied) Development of targeted therapies for triple-negative breast cancer (TNBC) has failed at least in part because of the heterogeneity of these poor prognosis cancers. To identify common dependencies of basal-like TNBCs, we performed a targeted siRNA lethality screen in 7 human breast cancer cell lines focusing on 154 previously identified dependency genes of one basal-A TNBC line. Thirty genes were shared basal-A TNBC dependencies. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 23 Samples
FTP download: GEO (CSV, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354957
Series		Accession: GSE90519	ID: 200090519

2441. Identification of PRMT5-dependent genes in ESA+CD24lowCD44+ MCF7 cells
(Submitter supplied) PRMT5 has been associated with poor prognosis in breast cancer. Here, we identify genes which are dependent on PRMT5 expression in MCF7 ESA+CD24lowCD44+ breast cancer stem cells by RNA-seq
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/GSE107762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421322
Series		Accession: GSE107762	ID: 200107762

2442. Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 24h in the presence of androgen
(Submitter supplied) The aim of this study was to use NGS RNAseq deep-sequencing in order to characterize the polyadenylated mRNAs and lncRNAs expressed in LNCaP cells treated with androgen hormone compared with untreated LNCaP cells (GSE79301). Trimmed reads were mapped using the hg19 genome with TopHat v.2.0.12 and Bowtie v.2.2.3. The assembly was guided by a custom GTF file created with transcripts fromhuman lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (GTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102305/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397388
Series		Accession: GSE102305	ID: 200102305

2443. Combinatorial Reprogramming of Estrogen Signaling  by the Nuclear Receptor Family 3C
(Submitter supplied) Estrogen receptor (ER) positive breast cancers exist in a complex environment of steroid hormones and their cognate receptors. Receptors for estrogens, progestogens (PR), androgens (AR), glucocorticoids (GR) and mineralocorticoids (MR) are variably expressed in these hormone- sensitive breast cancers. Clinical translation of crosstalk among these receptors has been limited by an incomplete understanding of ER reprogramming by PR, GR, AR and MR (NR3C receptors). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 GPL20301 62 Samples
FTP download: GEO (BED, CSV, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99626/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389107
Series		Accession: GSE99626	ID: 200099626

2444. Downregulation of DDX5/DDX17 and REST
(Submitter supplied) We aimed at analysing the effect of RNA helicases DDX5 and DDX17 and of the transcription factor REST on gene expression in the human SH-SY5Y neuroblastoma cell line (European Collection of Cell Cultures, ECACC), which was cultured as recommended by the supplier.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98871/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386482
Series		Accession: GSE98871	ID: 200098871

2445. T47D xenografts treated with various combinations of ER- and PR-targeting therapies
(Submitter supplied) Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18573 17 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80619/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319523
Series		Accession: GSE80619	ID: 200080619

2446. PR isoform-specific ER and PR chromatin binding and gene expression observed in-vitro in breast cancer cells.
(Submitter supplied) Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR dictates distinct ER and PR chromatin binding and differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 50 Samples
FTP download: GEO (BED, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80358/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318685
Series		Accession: GSE80358	ID: 200080358

2447. The myelin protein PMP2 is regulated by SOX10 and drives melanoma cell invasion
(Submitter supplied) The transcription factor SRY(sex related protein-Y)-box10 (SOX10) plays a key role in the development of melanocytes and peripheral glial cells from neural crest precursors. Recently, we and other groups found SOX10 to be involved in melanoma initiation, proliferation, invasion, and survival. However, specific mediators which impart the oncogenic role of SOX10 in melanoma remain widely unknown. To identify potential target genes of SOX10, we performed RNA sequencing to analyze genome-wide expression alterations after ectopic expression of SOX10. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79988/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317571
Series		Accession: GSE79988	ID: 200079988

2448. The role of PRMT5/WDR77 complex in promoting breast cancer 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: GPL9052 8 Samples
FTP download: GEO (BED) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75743/
Series		Accession: GSE75743	ID: 200075743

2449. The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq_HPTB]
(Submitter supplied) Comprehensive RNA-seq experiments in DMSO and HPTB (inhibitor of PRMT5) treated cells delineate the role of PRMT5 complex in promoting breast cancer oncogenesis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75742/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305260
Series		Accession: GSE75742	ID: 200075742

2450. The role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis [RNA-Seq]
(Submitter supplied) Comprehensive RNA-seq experiments in control and PRMT5 and WDR77 shRNA infected cells delineate the role of PRMT5/WDR77 complex in promoting breast cancer oncogenesis
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305261
Series		Accession: GSE75741	ID: 200075741

2451. RNA-seq in acute myeloid leukemia (AML) cells with and without knockdown of METTL14
(Submitter supplied) To dissect the mechanism underlying the oncogenic function of METTL14 in AML, we performed deep sequencing for mRNA isolated from MM6 and NB4 cells with and without knockdown of METTL14
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97443/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381786
Series		Accession: GSE97443	ID: 200097443

2452. N6-methyladenosine (m6A) sequencing of messenger RNAs in acute myeloid leukemia (AML) cells with and without knockdown of METTL14 [m6A-seq]
(Submitter supplied) To dissect the mechanism underlying the oncogenic function of METTL14 in AML, we performed m6A RNA immunoprecipitation and deep sequencing for mRNA isolated from MM6 and NB4 cells with and without knockdown of METTL14
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/GSE97nnn/GSE97408/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381699
Series		Accession: GSE97408	ID: 200097408

2453. Effect of RBP2 on MCF7 breast cancer cells (RNA-seq)
(Submitter supplied) RNA-sequencing analysis of RBP2 overexpressing MCF7 cell lines. RBP2 (also known as JARID1A), a member of the JARID1 family of histone H3 lysine K4 demethylases, has been considered to have an oncogenic potential in several cancer including breast cancer. Results provide insight into the transcriptional regulation of RBP2 in estrogen receptor positve breast cancer.
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/GSE92nnn/GSE92943/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356680
Series		Accession: GSE92943	ID: 200092943

2454. Genome-wide analysis of RNA-binding protein PSF-associated transcripts in prostate cancer
(Submitter supplied) Prostate cancer is the most common cancer in men and androgen receptor (AR) downstream signalings promote prostate cancer cell proliferation. PSF is an RNA-binding protein which is involved in AR signaling. To investigate the role of PSF, we performed RNA immunoprecipitation (RIP) and crosslinking immunoprecipitation (CLIP) sequence analysis in AR-positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells 22Rv1 and long term androgen deprivation (LTAD) cells to explore the differences of PSF function in prostate cancer progression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 22 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94243/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369120
Series		Accession: GSE94243	ID: 200094243

2455. Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.
(Submitter supplied) We report RNAseq data from subsequent passages of five organoid cultures.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108391/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA427119
Series		Accession: GSE108391	ID: 200108391

2456. c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Danio rerio; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL20828 GPL18573 27 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101297/
Series		Accession: GSE101297	ID: 200101297

2457. The cohesin complex prevents Myc-induced replication stress
(Submitter supplied) The cohesin complex is mutated in cancer and in a number of rare familiar syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 18 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89799/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353350
Series		Accession: GSE89799	ID: 200089799

2458. Hyperactive mTOR and MNK1 phosphorylation of eIF4E confer tamoxifen resistance and estrogen independence through selective mRNA translation reprogramming
(Submitter supplied) Tamoxifen resistant translational reprogramming is shown to be mediated by increased expression of eIF4E and its increased availability by hyperactive mTOR, and to require phosphorylation of eIF4E at Ser209 by increased MNK activity.
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/GSE107nnn/GSE107590/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420692
Series		Accession: GSE107590	ID: 200107590

2459. Gene expression changes in human melanoma cell lines compared to primary melanocytes
(Submitter supplied) Gene expression changes in 3 human melanoma cell lines were compared to freshly isolated normal primary melanocytes
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/GSE88nnn/GSE88741/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348439
Series		Accession: GSE88741	ID: 200088741

2460. RNA deep sequencing analysis of glioma stem cells(GSCs) and non-GSCs
(Submitter supplied) To explore potential molecular mechanisms underlying the temporal process of DNA damage and repair in CSCs, we utilized deep RNA sequencing to analyze the expression of DNA damage and repair-associated genes at the transcriptome level. Our gene set analysis of CSCs and matched non-CSCs revealed a stemness-associated upward trend of global gene expression, particularly in NHEJ, mismatch excision repair (MMR) and HR pathways.
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/GSE108nnn/GSE108322/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA423102
Series		Accession: GSE108322	ID: 200108322

2461. Mutational landscape of splicing genes and functional consequences across 33 cancer types
(Submitter supplied) Hotspot mutations in the spliceosome component genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of this pathway in cancer. However, a comprehensive survey of splicing factor mutations across tumor types has not yet been performed. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA) in order to discover recurrent mutations in spliceosome components, identifying 119 genes with significant non-silent mutation patterns, including mutation overrepresentation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100530/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392042
Series		Accession: GSE100530	ID: 200100530

2462. H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers
(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 (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95011/
Series		Accession: GSE95011	ID: 200095011

2463. H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers [Nalm-6]
(Submitter supplied) Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factors SF3B1, U2AF1, and SRSF2 that confer an alteration of function. Although cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function, clinical means to therapeutically target the spliceosome do not currently exist. Here, we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and selectively kills spliceosome-mutant epithelial and hematologic malignancies. 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/GSE94nnn/GSE94999/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375102
Series		Accession: GSE94999	ID: 200094999

2464. H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers [K562]
(Submitter supplied) Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factors SF3B1, U2AF1, and SRSF2 that confer an alteration of function. Although cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function, clinical means to therapeutically target the spliceosome do not currently exist. Here, we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and selectively kills spliceosome-mutant epithelial and hematologic malignancies. 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/GSE94nnn/GSE94528/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371421
Series		Accession: GSE94528	ID: 200094528

2465. Association with Aurora-A controls N-MYC-dependent promoter escape and pause release of RNA polymerase II during the cell cycle
(Submitter supplied) MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (RNAPII). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of RNAPII promoters and intergenic regions. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL10999 50 Samples
FTP download: GEO (BEDGRAPH, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78957/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314499
Series		Accession: GSE78957	ID: 200078957

2466. Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify
(Submitter supplied) Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL21311 16 Samples
FTP download: GEO (BED, GFF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108140/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422579
Series		Accession: GSE108140	ID: 200108140

2467. A 29-Gene and Cytogenetic Score for the Prediction of Resistance to Induction Treatment in Acute Myeloid Leukemia
(Submitter supplied) Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 250 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106291/
Series		Accession: GSE106291	ID: 200106291

2468. Class I histone deacetylases HDAC1, 2 and 3 are histone decrotonylases
(Submitter supplied) We characterize histone crotonylation in intestinal epithelium-derived cells through Mass spectrometry, ChIp-Seq and RNA-Seq approaches and show that this modification is removed by class I histone deacetylases, HDAC1, 2 and 3.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378641
Series		Accession: GSE96035	ID: 200096035

2469. Enzyme-free digital counting of endogenous circular RNA molecules in Formalin-Fixed Paraffin-Embedded tissues from patients with B-cell malignancies
(Submitter supplied) Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies. We quantified circular RNA expression by total RNA sequencing of four different Mantle Cell Lymphoma cell lines, REC-1, Granta-519, Z138 and UPN2 and the Multiple Myeloma cell line, H929.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20301 5 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422464
Series		Accession: GSE108111	ID: 200108111

2470. CSL RNA-Seq on HKC and SCC cell lines
(Submitter supplied) Down-modulation or loss-of-function mutations of the Notch 1 and 2 genes are associated with development of squamous cell carcinoma (SCC), a very frequent and therapy-resilient malignancy in skin, head/neck (H/N), lung and other surface epithelia. In this context, surprisingly little is known on the role of CSL (RBP-Jk), key effector of canonical Notch signaling endowed with intrinsic transcription repressive function. 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/GSE102nnn/GSE102762/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398638
Series		Accession: GSE102762	ID: 200102762

2471. KDM4 inhibition targets breast cancer stem 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: GPL11154 13 Samples
FTP download: GEO (BED, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95294/
Series		Accession: GSE95294	ID: 200095294

2472. KDM4 inhibition targets breast cancer stem cells [RNA-Seq]
(Submitter supplied) We treated breast cancer stemm cells (BCSC) with a KDM4 inhibitor
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/GSE95nnn/GSE95293/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376575
Series		Accession: GSE95293	ID: 200095293

2473. FOXO1 is an oncogenic mediator in AML1-ETO leukemia
(Submitter supplied) Transcriptome analysis by RNAseq of human CD34+ hematopoietic stem and progenitor cells transduced with empty vector control(MIT), AML1-ETO (AE), wildtype FOXO1 (F WT) or FOXO1 DNA binding deficient mutant (F DB). We find wildtype FOXO1 partially recapitulates gene signature of AML1-ETO
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81084/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320467
Series		Accession: GSE81084	ID: 200081084

2474. Extreme heterogeneity of influenza virus infection in single cells
(Submitter supplied) Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in production of viral gene transcripts -- viral transcripts compose less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. more...
Organism:	Homo sapiens; Influenza A virus (A/WSN/1933(H1N1))
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL24389 5 Samples
FTP download: GEO (FASTA, GTF, H5, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108041/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422274
Series		Accession: GSE108041	ID: 200108041

2475. Microenvironmental-derived Regulation of HIF-Signaling Drives Transcriptional Heterogeneity in Glioblastoma Multiforme
(Submitter supplied) The evolving and highly heterogeneous nature of malignant brain tumors underlies their limited response to therapy and poor prognosis. In addition to genetic alterations, highly dynamic processes such as transcriptional and metabolic reprograming play an important role in the development of tumor heterogeneity. The present study reports an adaptive mechanism in which the metabolic environment of malignant glioma drives transcriptional reprogramming. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 12 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108013/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422221
Series		Accession: GSE108013	ID: 200108013

2476. Epigenetic Therapy Increases Therapeutic Efficacy in Myeloproliferative Neoplasms  Through Inhibition of Aberrant Inflammatory Signaling
(Submitter supplied) The mechanisms that mediate transformation in MPN are not fully delineated and clinically utilized JAK inhibitors have limited ability to reduce disease burden or reverse myelofibrosis. Here we show that MPN progenitor cells are characterized by marked alterations in gene regulation through differential enhancer utilization, and identify Nfb signaling as a key pathway activated in malignant and non-malignant cells in MPN. more...
Organism:	Mus musculus; Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 39 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91062/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356762
Series		Accession: GSE91062	ID: 200091062

2477. The anti-leukemic effect of R-2HG depends on its acting as an m6A mRNA modifier-RNA Seq-PBS / R-2HG treatment
(Submitter supplied) RNA-seq from R-2HG sensitive leukemia cells treated with R-2HG or PBS.
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/GSE87nnn/GSE87189/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343812
Series		Accession: GSE87189	ID: 200087189

2478. The anti-leukemic effect of R-2HG depends on its acting as an m6A mRNA modifier-RNA Seq-Resistant, sensitive and healthy control
(Submitter supplied) To identify the potential genes/signaling pathways related to R-2HG sensitivity in leukemia cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87187/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343815
Series		Accession: GSE87187	ID: 200087187

2479. A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia
(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: GPL570 GPL16791 54 Samples
FTP download: GEO (CEL, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108004/
Series		Accession: GSE108004	ID: 200108004

2480. A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia [RNA-Seq]
(Submitter supplied) We demonstrate a promising approach to identify robust molecular markers for targeted treatment of acute myeloid leukemia. We show that our method outperforms several state-of-the-art approaches in identifying molecular markers replicated in validation data and predicting drug sensitivity accurately. Finally, we identify SMARCA4 as a marker and driver of sensitivity to topoisomerase II inhibitors, mitoxantrone and etoposide, in AML by showing that cell lines transduced to have high SMARCA4 expression reveal dramatically increased sensitivity to these agents.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 24 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108003/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA422203
Series		Accession: GSE108003	ID: 200108003

2481. Transcriptional profiles reflect the mutational mechanism by which Wnt signaling is activated in mouse tumors and predict outcome in colorectal cancer patients
(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 10 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103895/
Series		Accession: GSE103895	ID: 200103895

2482. 5hmC and gene expression data in breast cancer cell lines treated with an antioxidant
(Submitter supplied) In this study, we identify genes with enriched 5-hydroxymethyl-cytosine (5hmC) modifications correlated with gene expression in breast cancer cell lines treated with an antioxidant. Results of our differential analysis showed that treatment with an antioxidant caused significant changes to gene-localized 5hmC enrichment patterns in MDA-MB-468 breast cancer cells. The 5hmC enrichment results were validated in a set of patient specimens when compared with adjacent non cancer tissue.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103850/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407290
Series		Accession: GSE103850	ID: 200103850

2483. mRNA profiles of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E
(Submitter supplied) Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of U251 cells with endogenous Gcn5 depletion and reconstituted expression of WT Flag-rGcn5 or Flag-rGcn5 Y645A / endogenous DLST depletion and reconstituted expression of WT V5-rDLST or V5-rDLST R224A/K226E Transcriptomes. And quantitatively analyze the cell signaling pathways that regulated by the studied mutants. 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/GSE98nnn/GSE98050/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383809
Series		Accession: GSE98050	ID: 200098050

2484. Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia using Next-Generation Sequencing and Bioinformatics
(Submitter supplied) Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia, and long-term hypoxia were analyzed using next-generation sequencing. 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 (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107848/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421706
Series		Accession: GSE107848	ID: 200107848

2485. RNA-seq analysis of the role of HBO1 (KAT7/MYST2) in the ovarian cancer cell line UWB1.289.
(Submitter supplied) Analysis of change in transcriptosome after stable lentiviral HBO1 knockdown in UWB1.289 ovarian cancer cell line.
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/GSE101972/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396043
Series		Accession: GSE101972	ID: 200101972

2486. PRK1/PKN1 controls migration and metastasis of androgen-independent prostate cancer cells
(Submitter supplied) The aim of this study is to describe expression changes related to the metastatic behavior of PCa cells after siRNA-mediated knockdown of PRK1.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE64nnn/GSE64082/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA270076
Series		Accession: GSE64082	ID: 200064082

2487. circRNA-sequencing
(Submitter supplied) circRNA sequencing for 10 samples.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92322/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357241
Series		Accession: GSE92322	ID: 200092322

2488. CLCN2 Chloride Channel Mutations in Familial Hyperaldosteronism Type II
(Submitter supplied) Primary aldosteronism (PA), a common cause of severe hypertension, features constitutive production of the adrenal steroid aldosterone. We analyzed a multiplex family with familial hyperaldosteronism type II (FH-II) and 80 additional probands with unsolved early-onset PA. Eight probands had novel heterozygous variants in CLCN2, including two de novo mutations and four independent occurrences of the identical p.Arg172Gln mutation; all relatives with early-onset PA carried the CLCN2 variant found in probands. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107030/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418853
Series		Accession: GSE107030	ID: 200107030

2489. Bladder cancer associated mutations in RXRA activate peroxisome proliferator-activated receptors
(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 GPL21290 34 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107783/
Series		Accession: GSE107783	ID: 200107783

2490. Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation
(Submitter supplied) RXRA regulates transcription as part of a heterodimer with 14 other nuclear receptors, including the peroxisome proliferator-activated receptors (PPARs).   Analysis from the TCGA raised the possibility that hyperactive PPAR signaling, either due to PPAR gamma gene amplification or RXRA hot-spot mutation (S427F/Y) drives 20-25% of bladder cancers.  Here we characterize mutant RXRA, demonstrating it induces enhancer/promoter activity in the context of RXRA/PPAR heterodimers. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL21290 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107735/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA421314
Series		Accession: GSE107735	ID: 200107735

2491. Covalent inhibitor of the Rho family inhibits the migration of breast cancer cells
(Submitter supplied) Small GTPase proteins usually serve as molecular switches in various biological process, such as the proliferation, survival, and migration of cells. Mutations or aberrant activations of small GTPase proteins, such as Ras, are frequently observed in various kinds of cancers. Drug discovery efforts that target the Ras family proteins are making breakthroughs, while the discovery of efficient inhibitors that target the Rho family proteins is still stagnant. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106605/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417393
Series		Accession: GSE106605	ID: 200106605

2492. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators
(Submitter supplied) Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in shaping genome evolution and providing genetic substrates for evolving new regulatory functions. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease. more...
Organism:	Mus musculus; Homo sapiens
Type:		Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 104 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95374/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376803
Series		Accession: GSE95374	ID: 200095374

2493. Gene Expression Profiling of human and mouse melanoma cell lines after shRNA-mediated knockdown of JMJD2C or LSD1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL23227 GPL23479 9 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105166/
Series		Accession: GSE105166	ID: 200105166

2494. Gene Expression Profiling of melanoma cell lines after shRNA-mediated knockdown of JMJD2C or LSD1
(Submitter supplied) We hypothesize that knockdown of the H3K9 demethylases JMJD2C or LSD1 results in decreased proliferation and tumorigenic potential
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23227 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE105nnn/GSE105137/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414916
Series		Accession: GSE105137	ID: 200105137

2495. Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma
(Submitter supplied) Purpose: Utility of immunological treatment in cancer has increased; however, many patients do not respond to treatment. Identification of robust predictive biomarkers is required to correctly stratify patients. Although clinical trials based on adoptive T cell therapy (ACT) have yielded high response rates and many durable responses in melanoma, 50-60% of the patients have no clinical benefit. Herein, we searched for predictive biomarkers to ACT in melanoma. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 25 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100797/
Series		Accession: GSE100797	ID: 200100797

2496. Novel Targeting of Transcription and Metabolism in Glioblastoma
(Submitter supplied) Purpose: Glioblastoma (GBM) is highly resistant to treatment, largely due to disease heterogeneity and resistance mechanisms. We sought to investigate a promising drug that can inhibit multiple aspects of cancer cell survival mechanisms and become effective therapeutics for GBM patients.  Experimental Design: To investigate TG02, an agent with known penetration of the Blood-Brain Barrier, we examined the effects as single agent and in combination with temozolomide, a commonly used chemotherapy in GBM. 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/GSE107nnn/GSE107601/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420677
Series		Accession: GSE107601	ID: 200107601

2497. PD-L1 (CD274) overexpression effect on glioblastoma cell line U251
(Submitter supplied) The aim was to identify genes that were influenced by PD-L1 overexpression in glioblastoma 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/GSE107nnn/GSE107581/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA420727
Series		Accession: GSE107581	ID: 200107581

2498. Targeting EZH2 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: GPL11154 24 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85432/
Series		Accession: GSE85432	ID: 200085432

2499. Targeting EZH2 in MYCN-amplified Neuroblastoma [RNA-seq]
(Submitter supplied) Purpose:  Identify new targets in MYCN-amplified Neuroblastoma Methods: Kelly and LAN-1 neuroblastoma cells were treated in duplicate with 2 uM GSK126 (Excess Biosciences M60071-2) or DMSO for 2 or 5 days. RNA was extracted from cells with the RNeasy Kit (Qiagen). RNA libraries were prepared for sequencing using standard Illumina protocols. The pool of sixteen samples was sequenced on two lanes of an Illumina HiSeq, generating single end reads of 32-76 bp length. 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/GSE85nnn/GSE85431/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338447
Series		Accession: GSE85431	ID: 200085431

2500. Ivy Glioblastoma Atlas Project
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; SNP genotyping by SNP array
Platforms: GPL11154 GPL6801 305 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107560/
Series		Accession: GSE107560	ID: 200107560

2501. Ivy Glioblastoma Atlas Project (RNA-Seq)
(Submitter supplied) The Ivy Glioblastoma Atlas Project (Ivy GAP) is a detailed anatomically based transcriptomic atlas of human glioblastoma tumors.  As collaborators, the Ivy Foundation funded the Allen Institute and the Swedish Neuroscience Institute to design and create the atlas.  The Paul G. Allen Family Foundation also supported the project.  This resource consists of a viewer interface that resolves the manually- and machine-annotated histologic images (H&E and RNA in situ hybridization) at 0.5 µm/pixel, a transcriptome browser to view and mine the anatomically-based RNA-Seq samples, an application programming interface, help documentation that describes the methods and how to use the resource, as well as SNP array data and the supporting longitudinal clinical information and MRI time course data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 270 Samples
FTP download: GEO (CSV, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107559/
Series		Accession: GSE107559	ID: 200107559

2502. Transcriptome-wide analysis of the RNA content of purified Nanoblades
(Submitter supplied) Programmable nucleases have enabled rapid and accessible genome engineering in eukaryotic cells and living organisms. However, their delivery into target cells can be technically challenging when working with primary cells or in vivo. Using engineered murine leukemia virus-like particles loaded with Cas9/sgRNA ribonucleoproteins (“Nanoblades”), we were able to induce efficient genome-editing in cell lines and primary cells including human induced pluripotent stem cells, human hematopoietic stem cells and mouse bone-marrow cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 1 Sample
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418904
Series		Accession: GSE107035	ID: 200107035

2503. Engineered Nanointerfaces for Microfluidic Isolation and Molecular Profiling of Tumor-specific Extracellular Vesicles
(Submitter supplied) Tumor-EVs were captured on a nanostructured interface through immunoaffinity immobilization in a microfluidic channel containing herringbone (HB) structure for efficient mixing (EVHB-Chip).  Processing serum and plasma samples from glioblastoma multiforme (GBM) patients, isolated tumor EVs were analyzed using next-generation RNA sequencing analysis, and identified genes specific to glioblastoma as well as transcripts that are hallmarks for the four genetic subtypes of disease (e.g., classical, mesenchymal, neural, and pro-neural).
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/GSE106nnn/GSE106804/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418103
Series		Accession: GSE106804	ID: 200106804

2504. Transcriptional changes in pancreatic cancer cells associated with gemcitabine resistance
(Submitter supplied) The goal of this study was to determine the transcriptional changes in pancreatic cancer cells after treatment with gemcitabine.
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/GSE106nnn/GSE106336/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416329
Series		Accession: GSE106336	ID: 200106336

2505. Tamoxifen Resistance in Breast Cancer is Regulated by the EZH2-ERa-GREB1 Transcriptional Axis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
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/GSE103243/
Series		Accession: GSE103243	ID: 200103243

2506. The transcriptome effect of overexpressing EZH2 in MCF7
(Submitter supplied) Purpose: Increasing evidence suggests that epigenetic reprogramming contributes significantly to the development of endocrine therapy resistance in breast cancer. The goal of this work is to explore how the histone methyltransferase EZH2 interacts with ER signaling and drives the insensitiveness of breast cancer cells to the antagonistic effect of tamoxifen on ER activity. Therefore,  we comprehensively analyzed the transcriptional program regulated by EZH2 in EZH2 overexpressed MCF-7 cells. more...
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/GSE103nnn/GSE103242/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400606
Series		Accession: GSE103242	ID: 200103242

2507. 22Rv1 in vivo progression model
(Submitter supplied) Purpose: Even in last stage of metastatic castration-resistant prostate cancer, androgen receptor (AR) signaling remains active.To derive high metastatic prostate cancer (PCa), we labeled AR-positive but castration-resistant 22Rv1 PCa cells with luciferase gene (22Rv1-Luc2) and these cells were orthotopically implanted in mouse prostate for spontaneous progression. Methods:  2 × 10^5 of luciferase-expressing 22Rv1 cells (22Rv1-Luc2) cells were implanted in the anterior prostate of nude mice. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389750
Series		Accession: GSE99857	ID: 200099857

2508. Effects of WCE herbal extract on hormone-refractory PC-3 tumors
(Submitter supplied) Purpose: Androgen-deprivation therapy is the standard treatment for prostate cancer but fails in hormone-refractory prostate cancer. The anti-inflammatory plant Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Here, we evaluated the systemic antitumor effects of a standardized and effect-optimized Wedelia chinensis herbal extract (WCE) on hormone-refractory prostate cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99820/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389147
Series		Accession: GSE99820	ID: 200099820

2509. Super-Enhancers Promote Transcriptional Dysregulation in  Nasopharyngeal 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: GPL11154 23 Samples
FTP download: GEO (BW, FPKM_TRACKING, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95751/
Series		Accession: GSE95751	ID: 200095751

2510. Super-Enhancers Promote Transcriptional Dysregulation in  Nasopharyngeal Carcinoma [RNA-seq]
(Submitter supplied) Nasopharyngeal carcinoma (NPC) is an invasive cancer with particularly high  incidence in Southeast Asia and Southern China. The pathogenic mechanisms of NPC,  particularly those involving epigenetic dysregulation, remain largely elusive,  hampering the clinical management of this malignancy. To identify novel druggable  targets, we carried out an unbiased high-throughput chemical screening and observed  that NPC cells were highly sensitive to cyclin-dependent kinases (CDKs) inhibitors,  especially THZ1, a covalent inhibitor of CDK7. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (FPKM_TRACKING, TSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95750/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378262
Series		Accession: GSE95750	ID: 200095750

2511. The transcriptome effect of knocking down EZH2 in TamR MCF7L
(Submitter supplied) Purpose: Increasing evidence suggests that epigenetic reprogramming contributes significantly to the development of endocrine therapy resistance in breast cancer. The goal of this work is to explore how the histone methyltransferase EZH2 interacts with ER signaling and drives the insensitiveness of breast cancer cells to the antagonistic effect of tamoxifen on ER activity. Therefore,  we comprehensively analyzed the transcriptional program regulated by EZH2 in tamoxifen-resistant (TamR) MCF-7 cells. more...
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/GSE92nnn/GSE92316/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357207
Series		Accession: GSE92316	ID: 200092316

2512. Inhibition of TGFβRI as a therapy for GATA4 deficient lung 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
Platform: GPL16791 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85003/
Series		Accession: GSE85003	ID: 200085003

2513. Inhibition of TGFβRI as a therapy for GATA4 deficient lung cancers [RNA-seq]
(Submitter supplied) GATA4 is frequently epigenetically silenced in lung cancers. However, the impact of GATA4 inactivation on tumorigenesis and related therapeutic strategy remain to be determined. Through the genome-wide screening of tumor suppressing transcription factors, we demonstrate that GATA4 functions as an essential tumor suppressor in lung cancer in vitro and in vitro. Interestingly, ectopic GATA4 expression resulted in cellular senescence. 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/GSE85nnn/GSE85001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335853
Series		Accession: GSE85001	ID: 200085001

2514. Inhibition of TGFβRI as a therapy for GATA4 deficient lung cancers [patient samples]
(Submitter supplied) GATA4 is frequently epigenetically silenced in lung cancers. However, the impact of GATA4 inactivation on tumorigenesis and related therapeutic strategy remain to be determined. Through the genome-wide screening of tumor suppressing transcription factors, we demonstrate that GATA4 functions as an essential tumor suppressor in lung cancer in vitro and in vitro. Interestingly, ectopic GATA4 expression resulted in cellular senescence. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 8 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84852/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335372
Series		Accession: GSE84852	ID: 200084852

2515. Massively-parallel functional characterization of MAPK1 missense mutants
(Submitter supplied) Genome-directed oncology has the potential to revolutionize patient treatment, but is limited by an abundance of rare, uncharacterized and therapeutically uninformative somatic variants. To accelerate characterization of the “long tail” of rare somatic variants, we quantified the activity and drug responsiveness of virtually all possible (99.84%) missense variants in the Ser/Thr kinase MAPK1/ERK2. We identified recurrent and rare hypermorphic and loss-of-function alleles, revealing that variant activity is uncorrelated with mutational frequency. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 192 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79989/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330634
Series		Accession: GSE79989	ID: 200079989

2516. Single cell RNA-seq analysis of head and neck cancer
(Submitter supplied) To understand the diversity of expression states within head and neck cancers, we profiled 5902 single cells from 18 patients with oral cavity tumors by single cell RNA-seq
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 5901 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103322/
Series		Accession: GSE103322	ID: 200103322

2517. Stranded RNASeq of human mammary primary tumors ER+ and paired adjacent healthy tissues
(Submitter supplied) Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which are complementary and overlapping to those of protein-coding transcripts (PCT). NATs were punctually described as regulating gene expression, and are expected to act more frequently in cis than other ncRNAs that commonly function in trans. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103001/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399721
Series		Accession: GSE103001	ID: 200103001

2518. Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
(Submitter supplied) LCCC1122 is a window trial in stage I-IV TNBC patients scheduled to undergo definitive surgery (either lumpectomy, mastectomy or surgical resection of oligometastatic disease). Enrolled patients will receive 1.5 -2.0 mg of the MEK1/MEK2 inhibitor GSK1120212 (trametinib; Mekinist®) orally once daily for 7 days (with treatment initiation dependent on surgical schedule) prior to their surgery, with pre- and post- treatment tissue analyzed for kinome response and resistant signatures. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 28 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107502/
Series		Accession: GSE107502	ID: 200107502

2519. Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers
(Submitter supplied) This study aims to address the fundamental mechanism(s) underlying histone deacetylase inhibition in regulating gene expression and cytostatic responses in transformed and normal cells. 
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 49 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101708/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395241
Series		Accession: GSE101708	ID: 200101708

2520. Promoter-bound METTL3 maintains myeloid leukemia by m6A-dependent regulation of protein translation
(Submitter supplied) N6-methyladenosine (m6A) is an abundant internal RNA modification, in both coding and non-coding RNAs, catalyzed by the METTL3/METTL14 methyltransferase complex. We identified METTL3 as an essential gene for acute myeloid leukemia (AML) cell growth in two distinct genetic screens. Down-regulation of METTL3 results in cell cycle arrest, differentiation of leukemic cells and failure to establish leukemia in immunodeficient mice. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platforms: GPL18460 GPL20301 42 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94613/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371833
Series		Accession: GSE94613	ID: 200094613

2521. RNAseq analysis of NR0B1 LOF
(Submitter supplied) We report analysis of transcriptional chanages following RNAi depletion of NR0B1 or NRF2 depletion in NSCLC cell lines as determined by RNAseq. Additionally we also determine the genomic location of NR0B1 in NSCLC lines by Chip-Seq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 29 Samples
FTP download: GEO (BED, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89569/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352602
Series		Accession: GSE89569	ID: 200089569

2522. Exploiting drug addiction mechanisms to select against MAPKi resistant melanoma
(Submitter supplied) Melanoma resistant to MAPK inhibitors (MAPKi) displays loss of fitness upon experimental MAPKi withdrawal and, clinically, may be resensitized to MAPKi therapy after a drug holiday. Here, we uncovered and therapeutically exploited the mechanisms of MAPKi addiction in MAPKi-resistant BRAF MUT or NRAS MUT melanoma. MAPKi-addiction phenotypes evident upon drug withdrawal spanned transient cell-cycle slowdown to cell-death responses, the latter of which required a robust phosphorylated ERK (pERK) rebound. 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/GSE87nnn/GSE87326/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344340
Series		Accession: GSE87326	ID: 200087326

2523. Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate
(Submitter supplied) Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV-irradiation, RNA Polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions to promote uniform and accelerated scanning of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased sensing of damaged sites, as confirmed by RNAPII accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 43 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83763/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326947
Series		Accession: GSE83763	ID: 200083763

2524. Proteotranscriptomic profiling of potential E6AP targets in prostate cancer cells
(Submitter supplied) Prostate cancer is a common cause of cancer-related death in men. E6AP, an E3 ubiquitin ligase and a transcription cofactor, is elevated in a subset of prostate cancer patients. Genetic manipulations of E6AP in prostate cancer cells expose a role of E6AP in promoting growth and survival of prostate cancer cells in vitro and in vivo. However, the effect of E6AP on prostate cancer cells is broad and it cannot be explained fully by previously identified tumour suppressor targets of E6AP, promyelocytic leukemia protein and p27. 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/GSE107245/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419409
Series		Accession: GSE107245	ID: 200107245

2525. RNA-seq from human meningioma samples
(Submitter supplied) We performed RNA-seq on 42 meningioma samples isolated from human patients to characterize the transcriptome of these tumors
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 42 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101638/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395045
Series		Accession: GSE101638	ID: 200101638

2526. Gene expression changes associated with high density collagen microenviroment in cancer cells
(Submitter supplied) We report RNA sequencing data from 2 cancer cell line (fibrosarcoma, HT1080 and Breast cancer, MDA-MB-231) and one non-canceours cell line (human foreskin fibroblast HFF) embbeded in two different 3D collagen matrix environements. The topographical organization of collagen within the tumor ECM has been implicated in guiding cancer cell migration and independently predicts progression to metastasis. Here, we show that collagen matrices with small pores and short fibers, but not Matrigel, trigger a conserved transcriptional response and subsequent motility switch in cancer cells that results in formation of multicellular network structures. The response is not mediated by hypoxia, matrix stiffness, or bulk matrix density, but by matrix architecture and beta1 integrin upregulation. The transcriptional module associated with network formation is enriched for migration and vasculogenesis-associated genes that predicted survival in patient data across nine distinct tumor types. Evidence at the protein level of this gene module is found in patient tumors displaying a vasculogenic mimicry (VM) phenotype. Our findings link a collagen matrix-induced migration program to VM, and suggest that this process may be broadly relevant to metastatic progression in solid human cancers.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393881
Series		Accession: GSE101209	ID: 200101209

2527. mRNA and miRNA expression profiling of CUL4B knockdown in MKN45 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
Platforms: GPL13497 GPL11154 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90503/
Series		Accession: GSE90503	ID: 200090503

2528. Real-time observation of light-controlled transcription in living cells
(Submitter supplied) Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. 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/GSE103nnn/GSE103868/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407355
Series		Accession: GSE103868	ID: 200103868

2529. Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 102 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96867/
Series		Accession: GSE96867	ID: 200096867

2530. Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [RNA-Seq]
(Submitter supplied) Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression.  To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 52 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96860/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379957
Series		Accession: GSE96860	ID: 200096860

2531. Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus; Rattus norvegicus
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL20301 GPL21103 GPL14844 62 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107182/
Series		Accession: GSE107182	ID: 200107182

2532. Comprehensive analysis of Long non-coding RNA expression in dorsal root ganglion reveals cell type specificity and dysregulation following nerve injury [human iPS]
(Submitter supplied) Dorsal root ganglion (DRG) neurons provide connectivity between peripheral tissues and spinal cord. Transcriptional plasticity within DRG sensory neurons after peripheral nerve injury contributes to nerve repair but also leads to maladaptive plasticity, including the development of neuropathic pain. This study presents tissue and neuron specific expression profiling of both known and novel Long Non-Coding RNAs (LncRNAs) in rodent DRG following nerve injury. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL20301 32 Samples
FTP download: GEO (CSV, GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107181/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA419263
Series		Accession: GSE107181	ID: 200107181

2533. New insights into diagnosis and therapeutic options for proliferative hepatoblastoma
(Submitter supplied) Surgery and cisplatin-based treatment of hepatoblastoma (HB) currently guarantee the survival of 70-80% of patients. However, some important challenges remain in diagnosing high risk tumors and identifying relevant targetable pathways offering new therapeutic avenues. Previously, two molecular subclasses of hepatoblastoma tumors have been described, namely C1 and C2; C2 being the subgroup with the poorest prognosis, a more advanced tumor stage and the worst overall survival rate. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 62 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104766/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413799
Series		Accession: GSE104766	ID: 200104766

2534. GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer
(Submitter supplied) The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL16791 GPL18573 GPL15433 125 Samples
FTP download: GEO (BED, BIGWIG, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106695/
Series		Accession: GSE106695	ID: 200106695

2535. GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 2)
(Submitter supplied) The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. 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/GSE106nnn/GSE106694/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417694
Series		Accession: GSE106694	ID: 200106694

2536. GRHL2 is a key lineage determining factor which collaborates with FOXA1 to establish a targetable collateral pathway in the setting of endocrine therapy-resistant breast cancer (RNA-Seq data set 1)
(Submitter supplied) The estrogen receptor (ER) is expressed in the majority of luminal breast cancers and inhibition of its transcriptional activity with selective estrogen receptor modulators, selective estrogen receptor degraders and/or aromatase inhibitors is a standard approach used in the management of this disease. Despite the positive clinical impact of these interventions, de novo and acquired resistance limits the therapeutic lifespan of these classes of drugs. 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/GSE106nnn/GSE106681/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417666
Series		Accession: GSE106681	ID: 200106681

2537. Integrative genome-wide analysis in non-small cell lung cancer cells
(Submitter supplied) We used complementing high-throughput sequencing technologies, including RNA-seq, DNase I-seq, and ChIP-seq, to examine the distribution of DNase I hypersensitive sites and H3K4me2 histone marks, to infer transcription factor binding sites, to identify key pathways in Gefinitib resistant and sensitive cell lines, PC9R and PC9 respectively, and to verify that some of up-regulated genes in PC9R can be found in Gefinitib resistant patients, which indicated that our study has valid clinical relevance. more...
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 (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63356/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267557
Series		Accession: GSE63356	ID: 200063356

2538. Non-synchronized cell cycle transcriptomics in U2OS and HeLa cancer cells
(Submitter supplied) Sorting U2OS and HeLa cells genetically modified with the Fucci System allowed us to separate cells according to cell cycle progression followed by RNA Sequencing to characterize the oscillating transcriptome in cells without the need for chemical synchronization.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 15 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104736/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413699
Series		Accession: GSE104736	ID: 200104736

2539. 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations
(Submitter supplied) Hi-C technique has been widely applied to study the three-dimensional architecture of the whole genome. Genome structures such as compartment A/B, TAD (topologically associated domain) and chromatin loops can be identified from Hi-C data in both normal cells of human and other species, and are found to be associated with features such as epigenetic markers, DNA-binding proteins and gene expression. But such technique had been rarely used in cancer studies. Here we used Hi-C to study the aneuploid cancer genomic architecture in multiple myeloma cells. Our results indicate that Hi-C interaction matrix of cancer cells is affected by CNVs and should be adjusted for copy number. After correcting this CNV bias, we found a significant overlapping between the boundaries of CNV blocks and boundaries of TADs, which suggests that TAD boundaries are fragile sites for CNV breakpoints. In addition, the compartment A/B switching is associated with differential gene expression, from which we found important genes that are related with multiple myeloma. We build a 3D structure model of the aneuploidy genome and found that there are great changes both in the whole genome spatial interactome and local chromosome territories. In summary, our research builds the first 3D genome interaction maps of multiple myeloma and the first time notice this CNV-driven bias in Hi-C studies, which may deepen our understanding of changes in cancer 3D genome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (FPKM_TRACKING, TAR, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87585/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345243
Series		Accession: GSE87585	ID: 200087585

2540. Melanoma therapeutic strategies that select against resistance by exploiting MYC-driven evolutionary convergence
(Submitter supplied) Diverse pathways can drive resistance to BRAF and MEK inhibitors in BRAF mutant melanoma, suggesting that durable control of resistance will be a major challenge. By combining statistical modeling of genomic data from matched pre-treatment and post-relapse patient tumors with functional interrogation, we discovered that major pathways of resistance converge to activate the transcription factor c-MYC (MYC). more...
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/GSE99nnn/GSE99923/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390137
Series		Accession: GSE99923	ID: 200099923

2541. YY1 is a structural regulator of enhancer-promoter loops
(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; Other
Platforms: GPL17021 GPL13112 GPL16791 47 Samples
FTP download: GEO (CLOUPE, CSV, TSV, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99521/
Series		Accession: GSE99521	ID: 200099521

2542. Harnessing BET inhibitor sensitivity reveals AMIGO2 as a melanoma survival gene.
(Submitter supplied) We utilize the transcriptional effects of BETi in melanoma and identify AMIGO2 as a direct target gene essential for melanoma cell survival both in vitro and in vivo. We further map the enhancer landscape of NHM and melanooma and show that genes regulated by super enhancers are expressed in higher levels, exihibit higher sensitivity to BETi, and over expressed in melanoma relative to NHM. In melanoma, AMIGO2 is regulated by super enhancers, which upon BETi lose their BRD2/BRD4 enrichment, resulting in AMIGO2 silencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 69 Samples
FTP download: GEO (BW, DIFF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94488/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369853
Series		Accession: GSE94488	ID: 200094488

2543. Inhibition of ERG Activity in Patient Derived Prostate Cancer Xenografts using the Small Molecule Inhibitor YK-4-279
(Submitter supplied) ERG activity was blocked using YK-4-279 in three subcutaneously implanted ERG+ (LuCaP 23.1, 86.2, and 35) and one ERG- (LuCaP 96) PDX.  Tumor volume (TV), body weight (BW), serum prostate specific antigen (PSA), and overall survival (OS) were compared to vehicle treated controls.  Changes in gene expression were assessed by RNASeq and tissue microarrays were constructed to assess necrosis, proliferation, apoptosis, microvessel density, and ERG expression.
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/GSE86nnn/GSE86387/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341588
Series		Accession: GSE86387	ID: 200086387

2544. Cohesin loss eliminates all loop domains [PRO-Seq]
(Submitter supplied) The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci – almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106886/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA418323
Series		Accession: GSE106886	ID: 200106886

2545. Transcription Factor Activating Protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma
(Submitter supplied) Despite the identification of MYCN amplification as an adverse prognostic marker in neuroblastoma, MYCN inhibitors have yet to be developed. Here, by integrating evidence from a whole genome shRNA library screen and the computational inference of master regulator proteins, we identify Transcription Factor Activating Protein 4 (TFAP4) as a critical effector of MYCN amplification in neuroblastoma, providing a novel synthetic lethal target. 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/GSE102nnn/GSE102652/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398270
Series		Accession: GSE102652	ID: 200102652

2546. Simultaneous enumeration of cancer and immune cell types from tumor gene expression data
(Submitter supplied) Cancers are composed of various cell types. We present an efficient algorithm to simultaneously Estimate the Proportion of Immune and Cancer cells (EPIC) from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. 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/GSE93nnn/GSE93722/
Series		Accession: GSE93722	ID: 200093722

2547. Network-based, cross-cohort discovery of transcriptional mechanisms presiding over maintenance of high-risk neuroblastoma subtype state
(Submitter supplied) Network-based analysis of neuroblastoma samples from two large cohorts identified master regulator proteins controlling the transcriptional state of three high-risk molecular subtypes. In particular, a TEAD4-MYCN positive feedback loop emerged as the core regulatory motif of a small protein module presiding over implementation and stability of the subtype associated with MYCN amplification. Specifically, MYCN transcriptionally activates TEAD4, which in turn activates MYCN both transcriptionally and post-translationally. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 16 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84389/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329050
Series		Accession: GSE84389	ID: 200084389

2548. SMAD2/3 are redirected to novel sites in MCF10A MII after prolonged TGFβ stimulation
(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 18 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83788/
Series		Accession: GSE83788	ID: 200083788

2549. JUNB is a critical AP1 component for SMAD2/3 binding after TGFβ stimulation [RNA-seq]
(Submitter supplied) We performed SMAD2/3 ChIP-seq analysis in MCF10A MII cells. To validate whether the changes in SMAD2/3 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analysis after short and long periods of TGFβ stimulation (0, 1.5h and 16h) in MII cells. In addition, we revealed that JUNB is a critical AP1 component for SMAD2/3 binding after TGFβ stimulation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 9 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83786/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326979
Series		Accession: GSE83786	ID: 200083786

2550. Transcriptome sequencing of 15 normal lung parenchyma (NL), 17 atypical adenomatous hyperplasia (AAH) and 16 lung adenocarcinoma (LUAD) samples from 17 patients
(Submitter supplied) We sought to characterize expression profiles signifying the development of atypical adenomatous hyperplasia (AAH) from normal lung parenchyma (NL), and its progression to lung adenocarcinomas (LUAD).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102511/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397914
Series		Accession: GSE102511	ID: 200102511

2551. The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [RNA-seq]
(Submitter supplied) Using chromatin conformation capture methods, we learned that the latent episome of the human Epstein-Barr virus (EBV) displays preferential chromosome association that correlates with gene density. The episome avoids gene-rich chromosomes and favors gene-poor chromosomes. Kaposi’s sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not, suggesting limited evolutionary conservation of this strategy. more...
Organism:	Homo sapiens; Human gammaherpesvirus 4
Type:		Expression profiling by high throughput sequencing
Platforms: GPL23362 GPL23185 2 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98122/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384033
Series		Accession: GSE98122	ID: 200098122

2552. Patient-derived organoid cultures model human primary liver cancer in vitro
(Submitter supplied) The study of human liver cancer has been hampered by the lack of reliable models that faithfully recapitulate the physiopathology of the patient’s original tumour ex vivo. Here, we describe the first culture system to allow the establishment and long-term expansion of human primary liver cancer (PLC) organoids (called tumoroids) from the three most common PLC subtypes: Hepatocellular carcinoma (HCC), Cholangiocarcinoma (CC) and mixed HCC/CC tumours (CHC). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18460 GPL20301 59 Samples
FTP download: GEO (TXT, VCF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84073/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327939
Series		Accession: GSE84073	ID: 200084073

2553. EZH2-bound RNAs associated with progression of prostate cancer
(Submitter supplied) Through high-throughput RNA immunoprecipitation sequencing (RIP-seq), we discovered that EZH2 protein associates with messenger RNAs of a number of genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63230/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA267022
Series		Accession: GSE63230	ID: 200063230

2554. Mutational landscape of aggressive natural killer-cell leukemia and drug profiling highlight JAK-STAT signaling as a therapeutic target in NK-cell malignancies
(Submitter supplied) Cell lines derived from NK cell neoplasms were characterized using RNA sequencing and high-throughput drug sensitivity profiling to identify therapeutically actionable drivers in malignant NK cells.
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/GSE106nnn/GSE106391/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416701
Series		Accession: GSE106391	ID: 200106391

2555. The stress granule transcriptome reveals principles of mRNA accumulation in stress granules.
(Submitter supplied) Stress granules are mRNA-protein assemblies formed on nontranslating mRNAs. Stress granules are important in the stress response, related to neuronal mRNP granules, and aberrant stress granules contribute to some degenerative diseases.  By RNA-Seq and single molecule FISH, we describe the stress granule transcriptome in both yeast and mammalian cells. This reveals that while essentially every mRNA, and some ncRNAs, can be targeted to stress granules, the efficiency of targeting can vary from <1% to 73%. more...
Organism:	Saccharomyces cerevisiae; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19756 GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99304/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388080
Series		Accession: GSE99304	ID: 200099304

2556. Anti-Warburg effect elicited by mitochondrial biogenesis drives differentiation of glioblastoma cells into astroglial cells
(Submitter supplied) Glioblastoma (GBM) is among the most aggressive of human cancers. Although differentiation therapy has been proposed to be potential approach to treat GBM, the mechanisms of induced differentiation remain poorly defined. Here, we established the induced differentiation model of GBM by using cAMP activators, which specifically directed GBM into astroglia. Next, transcriptomic and proteomic analyses uncovered oxidative phosphorylation and mitochondrial biogenesis were involved in induced differentiation of GBM. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89745/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353078
Series		Accession: GSE89745	ID: 200089745

2557. RNA-seq analysis of gene expression in scramble and GPR126 knockdown colon cancer cells (HT-29)
(Submitter supplied) Purpose: Identify genes regulated by GPR126 in colon cancer cells by RNA-seq analysis Methods: Use shRNAs to knock down GPR126 in HT-29 cells, total RNAs from scramble group (NC) and GPR126 knockdown group (Sh1) were subjected to RNA-sequencing. Results: Around 700 transcriptomes were up-regulated in GPR126 knockdown HT-29 cells, and 14000 transcriptomes were down-regulated in GPR126 knockdown HT-29 cells.GPR126 mainly regualtes genes from DNA synthesis and cell cycle-related pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 2 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106696/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417696
Series		Accession: GSE106696	ID: 200106696

2558. PolyA RNA-seq from HCT116 (WT and CDK8as/as) cells in normoxia or hypoxia and treated with DMSO or 3MB-PP1
(Submitter supplied) To determine the impact of CDK8 kinase activity on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (CDK8wt/wt and CDK8as/as) in the presence of absence of 3MB-PP1 to specifically inhibit analog senstitive (as) CDK8.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 16 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101526/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394729
Series		Accession: GSE101526	ID: 200101526

2559. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers
(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 23 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99906/
Series		Accession: GSE99906	ID: 200099906

2560. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [RNA-Seq]
(Submitter supplied) Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to impact gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that can prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor a binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene 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/GSE99nnn/GSE99641/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389131
Series		Accession: GSE99641	ID: 200099641

2561. Inhibition of H3K4 demethylation induces autophagy in cancer cell lines
(Submitter supplied) Epigenetic factors and related small molecules have emerged to be strongly involved in autophagy process. Here we report that two inhibitors of histone H3K4 demethylase KDM1A/LSD1, 2-PCPA and GSK-LSD1, are able to induce autophagy in multiple cell lines. The two small molecules induced accumulation of LC3II, formation of autophagosome, fusion of autophagosome with lysosome and SQSTM1/p62 degradation. 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/GSE89nnn/GSE89672/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352870
Series		Accession: GSE89672	ID: 200089672

2562. Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes
(Submitter supplied) Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Wild Type astrocytes transcriptome profiling (RNA-seq) to AXL-/- astrocytes transcriptome profiling and to explore the mechanism by which AXL interferes with type I IFN signaling in WT astrocytes. We performed an RNA-Seq analysis of WT and AXL-/- U-251MG cells in the absence of ZIKV. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106545/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA417188
Series		Accession: GSE106545	ID: 200106545

2563. Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous measurement of telomere length and RNA-seq in the same human ES cell
(Submitter supplied) Telomere length heterogeneity in various cell types including stem cells and cancer cells has been recognized. Cell heterogeneity also is found in pluripotent stem cells such as embryonic stem cells (ESCs). The implication and mechanisms underlying the heterogeneity remain to be defined. We have optimized a robust method that can simultaneously measure telomere length coupled with RNA-sequencing analysis (scT&R-seq) in the same human ES cell. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 121 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385809
Series		Accession: GSE98644	ID: 200098644

2564. Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples
(Submitter supplied) We performed whole transcriptome analysis of osteosarcoma bone samples. Initially we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded (FFPE) samples to verify the RNAseq results. The use of FFPE samples allowed to analyse the effect of chemotherapy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20148 51 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389279
Series		Accession: GSE99671	ID: 200099671

2565. Oncolytic reactivation of KSHV as a therapeutic approach for primary effusion lymphoma: RNA-sequencing of PEL cell lines during KSHV reactivation
(Submitter supplied) Primary effusion lymphoma (PEL) is an aggressive subtype of non-Hodgkin lymphoma caused by Kaposi’s sarcoma-associated herpesvirus infection, which is most commonly seen in HIV-positive patients. Induction of HIV reactivation by external stimuli in the presence of highly active anti-retroviral therapy (HAART) has been examined for its efficacy to eradicate latently infected HIV. Similary, lytic activation of viruses from latently infected tumor cells with anti-cancer drugs represents an effective strategy of anti-neoplastic therapy, through the induction of oncolysis by viral replication, stimulation of immune responses to the viral lytic antigens, and intrinsic effects of cancer drugs. 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/GSE89nnn/GSE89478/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352335
Series		Accession: GSE89478	ID: 200089478

2566. High-Throughput Drug Screening identifies Pazopanib and Clofilium tosylate as effective treatments for malignant rhabdoid tumors
(Submitter supplied) mRNA expression in two different cell lines (DEV and G401) and two conditions (CLOFILIUM and DMSO) were assessed using the Illumina HiSeq2500 plateform in order to detect genes that are differentially expressed in CLOFILIUM condition compared to control (DMSO)
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/GSE102nnn/GSE102467/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397908
Series		Accession: GSE102467	ID: 200102467

2567. RNAseq of normal associate fibroblasts after treatment with large oncosomes from prostate cancer cells
(Submitter supplied) In order to detect the alteration in the transcriptomic profile of fibroblasts exposed to the large oncosomes and detemine the transcription factor responsible for those alteration we performed whole RNA sequncing with and without treatment with large oncosomes. Deep sequencing data were generated in duplicate using a NextSeq 500 platform (Illumina) using 75 single-end sequencing obtaining about 20 million reads per sample. 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/GSE87nnn/GSE87563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345199
Series		Accession: GSE87563	ID: 200087563

2568. Overexpression of TREM2 in human gastric cancer cells
(Submitter supplied) In order to investigate the molecular mechanisms underlying the role of TREM2 in gastric cancer, deep sequencing to profile global gene expression of MGC-803 cells with TREM2 overexpression was performed.
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/GSE106nnn/GSE106387/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416663
Series		Accession: GSE106387	ID: 200106387

2569. Improved Detection of Circulating Epithelial Cells in Patients with Intraductal Papillary Mucinous Neoplasms
(Submitter supplied) Circulating epithelial cells (CECs) were purified using a microfluidic device from healthy donors, patients bearing intraductal papillary mucinous neoplasms, or pancreatic ductal adenocarcinoma and their transcriptomes were sequenced.
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/GSE103nnn/GSE103152/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400365
Series		Accession: GSE103152	ID: 200103152

2570. The hepatitis C viral protein NS5A stabilizes growth-regulatory human transcripts
(Submitter supplied) Numerous mammalian proto-oncogene and other growth-regulatory transcripts are upregulated in malignancy due to abnormal mRNA stabilization.  In hepatoma cells expressing a hepatitis C virus (HCV) subgenomic replicon, we found that the viral nonstructural protein 5A (NS5A), a protein known to bind to viral RNA, also bound specifically to human cellular transcripts that encode regulators of cell growth and apoptosis, and this binding correlated with transcript stabilization. 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/GSE102nnn/GSE102910/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399262
Series		Accession: GSE102910	ID: 200102910

2571. A prostate cancer risk element functions as a repressive loop that regulates HOXA13
(Submitter supplied) Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ~42% of the susceptibility to PCa. To understand the causal genetic factors associated with PCa, we have focused on a PCa risk region located at 7p15.2. We performed Hi-C analysis and demonstrated that this region has long range interactions with the HOXA locus, located ~873 kb away. Using the CRISPR/Cas9 system, we deleted a 4 kb region encompassing several prostate cancer risk-associated SNPs and performed RNA-seq to investigate transcriptomic changes in RWPE1 prostate cells lacking the regulatory element. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL21290 GPL11154 38 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98898/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386902
Series		Accession: GSE98898	ID: 200098898

2572. Expression profiling and occupancy after knockdown or over-expression of HFN1A or HNF4G in prostate 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
Platform: GPL11154 38 Samples
FTP download: GEO (NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85559/
Series		Accession: GSE85559	ID: 200085559

2573. Single-Cell RNAseq analysis of diffuse neoplastic infiltrating cells at the migrating front of human glioblastoma
(Submitter supplied) We used single-cell RNAseq to investigate the heterogeneity of glioblastoma tumors and assess differential expression between cells within and in proximity of the tumor.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 3589 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84465/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330719
Series		Accession: GSE84465	ID: 200084465

2574. Agonistic targeting of TLR1/TLR2 induces p38 MAPK-dependent apoptosis and NfkB-dependent differentiation of AML cells
(Submitter supplied) Acute myeloid leukemia (AML) is associated with poor survival and there is a strong need to identify disease vulnerabilities that might reveal new treatment opportunities. Here, we found that Toll-like receptor 1 (TLR1) and TLR2 are upregulated on primary AML CD34+CD38- cells relative to corresponding normal bone marrow cells. Activating the TLR1/TLR2 complex by the agonist Pam3CSK4 in MLL-AF9 driven human AML, resulted in induction of apoptosis by p38 MAPK-dependent activation of Caspase 3 and myeloid differentiation in a NFκB-dependent manner. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92744/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358508
Series		Accession: GSE92744	ID: 200092744

2575. YEATS2 Links Histone Acetylation to Tumorigenesis of Non-small Cell Lung Cancer
(Submitter supplied) Recognition of modified histones by “reader” proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. For instance, bromodomain-containing proteins bind to acetylated histones and regulate chromatin dynamics and gene expression. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90781/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355886
Series		Accession: GSE90781	ID: 200090781

2576. NR2E3 gene networks are associated with AHR signaling pathways
(Submitter supplied) In order to identify NR2E3-specific gene expression pattern in liver cancer cell line, small hairpin RNA for NR2E3 was transfected in HepG2 human liver cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79463/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315878
Series		Accession: GSE79463	ID: 200079463

2577. A network-based strategy for prioritizing hits from chemical screening data by leveraging genetic, epigenetic and transcriptional datasets
(Submitter supplied) Small molecule screens are widely used to prioritize compounds for development of pharmaceuticals and to reveal pathways altered in biological processes.  However, interpreting the results of these screens is very challenging since in almost all cases, the compounds are highly promiscuous.  Here we present a network-based strategy for analyzing molecular screening data.  We report a screen for kinase inhibitors that synergize with gemcitabine, the first-line chemotherapy treatment for pancreatic cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70810/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA289622
Series		Accession: GSE70810	ID: 200070810

2578. Transcriptome analysis of PC9 cells with gefitinib or/and hypoxia treatment and comparison with gefitinib resistant PC9 cells and ALDH positive PC9 cells
(Submitter supplied) Inevitable gefitinib resistance and relapse of the disease was the biggest hurdle to NSCLC treatment. Importantly, the role of hypoxia in solid tumor tissues in vivo in gefitinib acquired resistance and its relationship to lung cancer stem cells (LCSCs) has not been fully elucidated. Here, the PC9 cells were treated with short term gefitinib or/and hypoxia, also, PC9 gefitnib resistant (PC9-GR) cell line was established and ALDH positive PC9 cells were sorted by FACs. 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/GSE69nnn/GSE69599/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285956
Series		Accession: GSE69599	ID: 200069599

2579. Syndecan-1 controls lung tumorigenesis by regulating microRNAs packaged in exosomes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 14 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106304/
Series		Accession: GSE106304	ID: 200106304

2580. Syndecan-1 controls lung tumorigenesis by regulating microRNAs packaged in exosomes [EKVX]
(Submitter supplied) We evaluated the effect of syndecan-1 in various cell-based and animal models of lung cancer and found that lung tumorigenesis was promoted when cells lose syndecan-1 expression. We also demonstrate that syndecan-1 (or lack thereof) alters the microRNA (miRNA) cargo carried within exosomes exported from lung cancer cells. Analysis of the changes in miRNA expression identifies a distinct shift toward augmented pro-cancerous signaling, which are consistent with the changes found in lung adenocarcinoma. 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/GSE106303/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA416253
Series		Accession: GSE106303	ID: 200106303

2581. H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Human RNA-Seq]
(Submitter supplied) Gain-of-function mutations in histone 3 (H3) variants are found in a large proportion of pediatric high-grade gliomas (pHGG) and are often associated with p53 loss and PDGFRA amplification. However, a lack of faithful models has hampered investigation of disease mechanisms and preclinical development. Here, we describe a somatic mouse model of H3.3K27M-driven HGG, which faithfully recapitulates human H3.3K27M pHGG. 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/GSE95nnn/GSE95277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376547
Series		Accession: GSE95277	ID: 200095277

2582. H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas
(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
4 related Platforms 63 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95169/
Series		Accession: GSE95169	ID: 200095169

2583. Gene expression profile of multiple myeloma cell lines treated with CB-5083
(Submitter supplied) The goal was to determine the gene expression differences between CB-5083 and Bortezomib treated multiple myeloma cell lines Inhibition of the AAA ATPase, p97, was recently shown to be a novel method for targeting the ubiquitin proteasome system (UPS) and CB-5083, a first in class inhibitor of p97, has demonstrated broad antitumor activity in a range of both hematological and solid tumor models. Here, we show that CB-5083 has robust activity against multiple myeloma (MM) cell lines and a number of in vivo MM models. 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/GSE101nnn/GSE101923/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395929
Series		Accession: GSE101923	ID: 200101923

2584. RNAseq analysis of genes regulated by GDE2 in neuronal cells
(Submitter supplied) We analyze differentially expressed genes in wild-type versus GDE2 knockdown neuroblastoma 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/GSE74nnn/GSE74345/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA299789
Series		Accession: GSE74345	ID: 200074345

2585. NR4A1 Inhibition Synergizes with Ibrutinib in Killing Mantle Cell Lymphoma Cells
(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to identify NR4A1 targets by RNA-seq and high-throughput data analysis and verify these genes by quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. Methods: Jeko/Rec-1 Cas9 control and NR4A1 sgRNA stable cell lines were generated with tet-on system vector, sg RNAs were induced for 48 hours after doxycycline addition, mRNA was extracted and used for RNA sequencing. 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/GSE106092/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA415591
Series		Accession: GSE106092	ID: 200106092

2586. UTX/KDM6A Loss Enhances the Malignant Phenotype of Multiple Myeloma and Sensitizes Cells to EZH2 inhibition
(Submitter supplied) In this project we analyze the transcriptome of the human multiple myeloma isogenic cell lines ARP-1 (UTX wild-type) and ARD (UTX null). The transcriptome is studied at baseline, upon restoration of UTX levels in ARD cells for 3 and 6 days, and upon treatment of the cell lines with the EZH2 inhibitor GSK343. Moreover, we analyzed the transcriptome of a ARD resistant cell line that we generated.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103567/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401933
Series		Accession: GSE103567	ID: 200103567

2587. The phosphatidylinositol 3-kinase pathway as a potential therapeutic target in bladder cancer
(Submitter supplied) Activation of the phosphatidylinositol 3-kinase (PI3K) pathway occurs in over 40% of bladder urothelial cancers. The aim of this study is to determine the therapeutic potential, the underlying action and resistant mechanisms of drugs targeting the PI3K pathway. Urothelial cancer cell lines and patient-derived xenografts (PDXs) were analyzed for alterations of the PI3K pathway and for their sensitivity to the small molecule inhibitor pictilisib alone and in combination with cisplatin and/or gemcitabine. more...
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/GSE101nnn/GSE101419/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394145
Series		Accession: GSE101419	ID: 200101419

2588. Suppression of adaptive responses to targeted cancer therapy by transcriptional 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
Platforms: GPL11154 GPL16791 166 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89129/
Series		Accession: GSE89129	ID: 200089129

2589. Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [RNA-seq]
(Submitter supplied) Large-scale genomic profiling efforts have facilitated the characterization of molecular alterations in cancers and aided the development of targeted kinase inhibitors for a wide array of cancer types. However, resistance to these targeted therapies invariably develops and limits their clinical efficacy. Targeting tumours with kinase inhibitors induces complex adaptive survival programs that promote the persistence of a fraction of the original cancer cell population, facilitating the eventual outgrowth of inhibitor-resistant tumour clones following clonal evolution. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 90 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89127/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350335
Series		Accession: GSE89127	ID: 200089127

2590. Survival of pancreatic cancer cells lacking KRAS function
(Submitter supplied) Activating mutations in the proto-oncogene KRAS are a hallmark of pancreatic ductal adenocarcinoma (PDAC), an aggressive malignancy with few effective therapeutic options. Despite efforts to develop KRAS-targeted drugs, the absolute dependence of PDAC cells on KRAS remains incompletely understood. Here we modeled complete KRAS inhibition using CRISPR/Cas-mediated genome editing. While KRAS knockout led to decreased in vitro proliferation and impaired in vivo tumorigenic growth, KRAS was dispensable in a subset of human and mouse PDAC cells. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 11 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292392
Series		Accession: GSE71876	ID: 200071876

2591. A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma
(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 25 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94503/
Series		Accession: GSE94503	ID: 200094503

2592. A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma [RNA-Seq]
(Submitter supplied) Ewing sarcoma usually expresses the EWS/FLI fusion transcription factor oncoprotein. EWS/FLI regulates myriad genes required for Ewing sarcoma development.  EWS/FLI binds GGAA-microsatellite sequences in vivo and in vitro, and these sequences provide EWS/FLI-mediated activation to reporter constructs, suggesting that they function as EWS/FLI-response elements.  Genomic GGAA-microsatellites are highly variable and polymorphic. more...
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/GSE94nnn/GSE94502/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374499
Series		Accession: GSE94502	ID: 200094502

2593. Identification of the networks that regulate human monocytic myeloid-derived suppressor cell differentiation into inflammatory macrophages
(Submitter supplied) Background: Monocytic myeloid-derived suppressor cells (mMDSC) support immune evasion of tumors by blocking tumoricidal T and NK cell response. Efforts to reverse mMDSC-mediated immunosuppression identified that the TLR7/8 agonist R848 induces their maturation into tumoricidal macrophages Purpose: The factors that determine whether human mMDSC differentiate into MACinflam or MACsuppress are unclear. 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/GSE105nnn/GSE105142/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414921
Series		Accession: GSE105142	ID: 200105142

2594. Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1
(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: GPL16791 5 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69507/
Series		Accession: GSE69507	ID: 200069507

2595. Chromatin-associated RNA-seq in MCF-7
(Submitter supplied) Deep sequencing of total RNA isolated from the chromatin fraction of MCF-7 cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69506/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA285756
Series		Accession: GSE69506	ID: 200069506

2596. The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing [RNA-seq]
(Submitter supplied) While transcription as regulated by histones and their post-translational modifications have been well described, the connection between histone variants and changes to transcription remains poorly characterized. Potentially important insight into this process is provided by the frequently occurring mutations of H3.3, leading to G34 substitutions in childhood glioblastoma and giant cell tumor of the bone (GCTB). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103559/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401867
Series		Accession: GSE103559	ID: 200103559

2597. mTOR kinase inhibition effectively decreases progression of a subset of neuroendocrine tumors that progress on rapalog therapy and delays cardiac impairment
(Submitter supplied) Inhibition of mTOR signaling using the rapalog everolimus is an FDA-approved targeted therapy for patients with lung and gastroenteropancreatic neuroendocrine tumors (NET). However, patients eventually progress on treatment, highlighting the need for additional therapies. We focused on pancreatic NETs (pNETs) and reasoned that treatment of these tumors upon progression on rapalog therapy, with an mTOR kinase inhibitor (mTORKi) such as CC-223 could overcome a number of resistance mechanisms in tumors and delay cardiac carcinoid disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 27 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102246/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397080
Series		Accession: GSE102246	ID: 200102246

2598. A class of GATA3 mutation reprograms the breast cancer transcriptional network through gain and loss of function
(Submitter supplied) A pioneer transcription factor, GATA3, is one of the most frequently mutated genes in breast cancer, yet the impact of these mutations is largely unknown. We generated a GATA3 mutant cell line (T47D wt/R330fs) by CRISPR. Mutation of one allele of GATA3 led to loss of binding and decreased expression at a subset of genes, including Progesterone Receptor.  At other loci, associated with epithelial to mesenchymal transition, gain of binding at a novel sequence motif correlated with increased gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 96 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99479/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388581
Series		Accession: GSE99479	ID: 200099479

2599. Microvesicle-mediated delivery of miR-1343: impact on markers of fibrosis
(Submitter supplied) We previously identified miR-1343 as a potent repressor of TGF-b signaling and fibrosis through the direct attenuation of both canonical TGF-b receptors. Here, we build upon our previous findings to better characterize the function of endogenous miR-1343 in normal biology. CRISPR/Cas9 techniques were used to delete the miR-1343 locus in A549 lung epithelial cells. Loss of miR-1343 was found to impact several processes and genes implicated in fibrosis and known to be TGF-b pathway effectors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387573
Series		Accession: GSE99209	ID: 200099209

2600. RNA-Seq comparative analysis of human neuroblastoma cells before and after their confrontation to the embryonic microenvironment
(Submitter supplied) We set up an innovative model for neuroblastoma that consists in using the chick embryo to place human neuroblastoma cells back to their original environment: the trunk neural crest. In this context, human neuroblastoma cells migrate towards sympathetic derivatives and form proliferative tumor masses. To assess the impact of the embryonic microenvironment on neuroblastoma cells gene program, we performed an RNASeq comparative analysis of neuroblastoma naïve cells and tumor masses settled in sympathetic derivatives.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91377/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356867
Series		Accession: GSE91377	ID: 200091377

2601. Formaldehyde facilitates cell transformation by compromising chromatin assembly
(Submitter supplied) Formaldehyde (FA) is an environmental and occupational chemical carcinogen. Recent studies demonstrated that exogenous FA caused only a modest increase in DNA adducts above levels caused by endogenous FA. This raised a possibility that epigenetic mechanisms might contribute to FA-mediated carcinogenicity. Here we report a drastic decrease of acetylation of N-terminal tails of the cytosolic histones following FA exposure, the modifications important for histone nuclear import and assembly into chromatin. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (GTF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87541/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345141
Series		Accession: GSE87541	ID: 200087541

2602. Alagille_Nodder
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL13112 GPL16512 22 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104876/
Series		Accession: GSE104876	ID: 200104876

2603. RNA Seq of Alagille liver biopsies
(Submitter supplied) Needle biopsies were performed to obtain liver samples from patients for clinical purposes from patients with Alagille syndrome. A small portion was snap frozen and later used for RNA sequencing analysis. Needle biospies from 5 patients with other liver disorders were included as controls.
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/GSE104nnn/GSE104873/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414076
Series		Accession: GSE104873	ID: 200104873

2604. Ribosome-free RNA sequencing of long noncoding RNAs and circular RNAs in lung adenocarcinoma
(Submitter supplied) Noncoding RNAs play important roles in various biological processes and diseases, including cancer. Expression profile of circular RNAs (circRNA) is largely unknown in lung adenocarcinoma. This study is designed to explore mRNA, long noncoding RNA (lncRNA), and circRNA in lung adenocarcinoma.
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/GSE104nnn/GSE104854/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA414037
Series		Accession: GSE104854	ID: 200104854

2605. Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation
(Submitter supplied) Elevated transcript expression of the endogenous retrovirus family HERV-K (HML-2) is seen in the majority of breast cancers, although the identity of the individual loci contributing to this expression as well as their mechanism of activation is unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we produced a complete profile of the HML-2 transcriptome before and after human mammary epithelial cell transformation.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 4 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84275/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328504
Series		Accession: GSE84275	ID: 200084275

2606. Differentially expressed LncRNAs and mRNA identified by SEQ analysis in colorectal cancer patients
(Submitter supplied) LncRNA plays an important role in gene regulation, but its impact on the pathogenesis of colorectal cancer and the biological function of cancer cells is unclear. In this study, we will use the next generation sequencing technique to study the differences of the expression profiles of lncRNA and mRNA in colorectal cancer tissues, analyzing the differentially expressed genes by GO/KEGG enrichment, and predicting the new lncRNAs’ function. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL21290 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104836/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413956
Series		Accession: GSE104836	ID: 200104836

2607. Activation of the p53 transcriptional program sensitizes cancer cells to Cdk7 inhibitors
(Submitter supplied) Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7as inhibitor to induce cell death. 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/GSE99nnn/GSE99794/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389616
Series		Accession: GSE99794	ID: 200099794

2608. AR-independent prostate cancer is sustained through FGF signaling
(Submitter supplied) Androgen receptor (AR) signaling is a distinctive feature of prostate cancer (PC) and represents the major therapeutic target for the treatment of metastatic disease. Though highly effective, AR antagonism has the potential to generate tumors that bypass a functional requirement for AR activity. We show here that a phenotypic shift has occurred in metastatic PCs with the emer-gence of a double-negative AR-null neuroendocrine-null phenotype that is notable for MAPK and FGF pathway activity. 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/GSE99nnn/GSE99381/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388341
Series		Accession: GSE99381	ID: 200099381

2609. CDK9-dependent RNA polymerase II pausing controls transcription initiation
(Submitter supplied) Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a ‘multi-omics’ approach to show that the duration of polymerase pausing generally limits the frequency of transcription initiation in human cells (‘pause-initiation limit’). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL18460 GPL16791 14 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96056/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378674
Series		Accession: GSE96056	ID: 200096056

2610. Effects of novel antiandrogens (enzalutamide and ARN-509) on global gene expression in castration-resistant prostate cancer (CRPC) xenograft model
(Submitter supplied) Global transcriptome analysis revealed altered expression of 291 genes, including mRNAs for several AR-interacting proteins and multiple enzymes involved in steroid metabolism. The data indicate that antiandrogens modify the androgen signaling in VCaP xenografts at multiple levels by reducing concentrations of active androgens, increasing AR expression and inducing alterations in the expression of AR interacting proteins, steroid metabolizing enzymes and AR downstream target genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 44 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95413/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377062
Series		Accession: GSE95413	ID: 200095413

2611. Clustering gene expression time series data using an infinite Gaussian process mixture model
(Submitter supplied) In order to identify and characterize novel human gene expression responses to glucocorticoids, we exposed the human lung adenocarcinoma cell line, A549, to the synthetic glucocorticoid dexamethasone for 1, 3, 5, 7, 9, and 11 hrs in duration as well as to a paired vehicle control, ethanol. We assayed gene expression with RNA-seq and clustered gene expression profiles using an infinite Gaussian process mixture model.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104714/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA413586
Series		Accession: GSE104714	ID: 200104714

2612. Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells
(Submitter supplied) We report RNA sequencing data from enriched prostate circulating tumor cells (CTCs) from clinical blood specimens. The goal is to examine the stability of RNA signatures as a function of whole blood preservation. Each blood sample was split into two equal portions; one portion was processed immediately (i.e., 0 hour) for CTC isolation; the other was preserved in 4 deg C, using methods described in this publication, for 24, 48, or 72 hours prior to CTC isolation. 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/GSE104nnn/GSE104209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412038
Series		Accession: GSE104209	ID: 200104209

2613. Integrator orchestrates RAS/ERK1/2 signaling transcriptional programs
(Submitter supplied) We investigated the occupancy of RNA PolII and INTS11 during the stimulation of EGF and compared with drug treated condition using inhibitors against MAPK pathway and Integrator. Additionally, we examined transcription by sequencing the chromatin-bound fraction of RNA.
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) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85089/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA336122
Series		Accession: GSE85089	ID: 200085089

2614. Cohesin loss eliminates all loop domains
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL20795 GPL16791 132 Samples
FTP download: GEO (BW, HIC, TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104334/
Series		Accession: GSE104334	ID: 200104334

2615. Global analysis of AGO2-bound RNAs in teratoma-derived fibroblasts
(Submitter supplied) Among the four Argonaute family members in mammals, only AGO2 protein retains endonuclease activity, and facilitates cleavage of target RNAs base-pairing with highly complementary guide RNAs. Despite the deeply conserved catalytic activity, only a small number of targets have been reported to extensively base pair with cognate miRNAs to be cleaved by AGO2. Here, we analyzed AGO2-bound RNAs by CrossLinking ImmunoPrecipitation (CLIP) of genetically modified cells that express epitope-tagged AGO2 from the native genomic locus. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 9 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93644/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361413
Series		Accession: GSE93644	ID: 200093644

2616. Genomic alterations activating KLF5
(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: GPL15520 56 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88978/
Series		Accession: GSE88978	ID: 200088978

2617. Genomic alterations activating KLF5 [RNA-Seq]
(Submitter supplied) Using RNA-seq to identify genes that regulated by KLF5 and KLF5 mutants
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88977/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349455
Series		Accession: GSE88977	ID: 200088977

2618. Ancestry as a potential modifier of gene expression in breast tumors from Colombian women
(Submitter supplied) Background: Differences in breast cancer outcomes according to race/ethnicity have been reported. Hispanic/Latino (H/L) populations are a genetically admixed and heterogeneous group, with variable fractions of European, Indigenous American and African ancestries. Some studies suggest that breast cancer-specific mortality is higher in U.S. Hispanic/Latinas compared to non-Hispanic Whites (NHW) even after adjustment for socioeconomic status and education. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 42 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101927/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395937
Series		Accession: GSE101927	ID: 200101927

2619. U1 snRNP telescripting regulates size-function stratified human genome
(Submitter supplied) This project looks into how U1 snRNP inhibition causes a loss of telescripting through premature cleavage and polyadenylation based on the size and function of human genes.
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 (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103252/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400626
Series		Accession: GSE103252	ID: 200103252

2620. CD15-positive tumor-derived glioblastoma 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: GPL11154 GPL16791 39 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103366/
Series		Accession: GSE103366	ID: 200103366

2621. Epigenetic silencing of the dual-role signal mediator, ANGPTL4 in tumor tissue and its overexpression in the urothelial carcinoma microenvironment
(Submitter supplied) To investigate the effect of ANGPTL4 expression on bladder cancer cells, expression profile was compared in BFTC 905 cells overexpressed with control vector vs human full length ANGPTL4 gene.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396903
Series		Accession: GSE102170	ID: 200102170

2622. Identification of differential expressed genes of JQ1 or JQ1+Bortezomib in colorectal cancer cells
(Submitter supplied) The bromodomain and extra-terminal domain inhibitors (BETi) are promising epigenetic drugs for the treatment of various cancers through suppression of oncogenic transcription factors including MYC. However, only a subset of CRC cells response to BETi, suggesting an intrinsic resistance to BETi in CRC. We investigated the effect of JQ1 on cell proliferation, apoptosis, angiogenesis and MYC expression in a panel of 11 CRC cells in vitro and in vivo. more...
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/GSE95nnn/GSE95513/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377308
Series		Accession: GSE95513	ID: 200095513

2623. Systematic identification of molecular pathways driving GBM invasion
(Submitter supplied) Glioblastoma multiforme (GBM) is the most prevalent and deadliest adult brain tumor. To systematically characterize the pathways governing brain invasion, we developed a three-dimensional (3D) ex vivo organotypic invasion model with clinical relevance to GBM. We used this model to enrich for highly invasive GBM cell population. Using next-generation sequencing to transcriptomically profile highly invasive and poorly invasive GBM cell populations, we have identified a network of extracellular matrix (ECM) components, including multiple collagens and collagen-interacting proteins, which are upregulated by invading GBM cells and strongly correlate in expression with clinical glioma progression outcomes. 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/GSE87nnn/GSE87535/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345047
Series		Accession: GSE87535	ID: 200087535

2624. Targeting Glioma Stem Cells through Combined BMI1 and EZH2 Inhibition [RNA-seq]
(Submitter supplied) Glioblastomas are lethal cancers defined by angiogenesis and pseudopalisading necrosis.  Here, we demonstrate that these features are associated with distinct transcriptional programs, with vascular regions showing a Proneural profile and hypoxic regions a Mesenchymal pattern.  As these regions harbor glioma stem cells (GSCs), we investigated the epigenetic regulation of these two niches.  Proneural, perivascular GSCs activated EZH2, whereas Mesenchymal GSCs in hypoxic regions expressed BMI1 protein, which promoted cellular survival under stress. more...
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/GSE86nnn/GSE86237/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341069
Series		Accession: GSE86237	ID: 200086237

2625. Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes
(Submitter supplied) Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. more...
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/GSE72nnn/GSE72577/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294385
Series		Accession: GSE72577	ID: 200072577

2626. ARID1A and ARID1B loss in TOV21G cells
(Submitter supplied) ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL18573 GPL16791 22 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101974/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396050
Series		Accession: GSE101974	ID: 200101974

2627. ARID1A and ARID1B loss in HCT116 cells
(Submitter supplied) ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL16791 GPL18573 52 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101966/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396039
Series		Accession: GSE101966	ID: 200101966

2628. NFATC2 knock-down on melanoma cell line A375
(Submitter supplied) RNA-seq on NFATC2 knock-down (siRNA) on melanoma cell line A375
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/GSE99nnn/GSE99466/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388509
Series		Accession: GSE99466	ID: 200099466

2629. Exploiting Prmt5-orchestrated intron detention signatures to treat splicing-addicted malignant glioma tumors
(Submitter supplied) The presence of introns within otherwise completely spliced mRNA molecules has been associated with splicing errors. Recent evidence however suggests that intron-based transcript inactivation is widespread and regulates the cytoplasmic availability of productive transcript isoforms. The regulatory and functional details of this process have remained unclear. We here present the arginine methyltransferase Prmt5 as the top hit from an in vivo RNAi screen for therapeutic vulnerabilities of malignant gliomas. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 6 Samples
FTP download: GEO (GFF3, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93813/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362466
Series		Accession: GSE93813	ID: 200093813

2630. Gene Expression Profile of human hepatocellular carcinoma by RNA sequencing
(Submitter supplied) The aim of the present study was to investigate biomarkers in the malignant process of HCC by high throughput sequencing.
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/GSE104nnn/GSE104310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412314
Series		Accession: GSE104310	ID: 200104310

2631. Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 
(Submitter supplied) We performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB-231) cells exposed to normoxic or hypoxic conditions and/or treated with an mTOR pathway inhibitor. Analysis of both the transcriptome and the translatome identified mRNA transcripts translationally activated or repressed by hypoxia in an mTOR-dependent or -independent manner. The mRNA populations of each sample were converted to cDNA libraries using the TruSeq protocol and then sequenced using a HiSeq 2000 machine. 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/GSE104nnn/GSE104193/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA412005
Series		Accession: GSE104193	ID: 200104193

2632. MYCL and EP400 are required for Max and MCPyV mediated gene activation
(Submitter supplied) To determine if MYCL or EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing shMYCL and two different EP400 shRNA -2, -3  and compared to ChIP-seq data using BETA analyses.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 15 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390939
Series		Accession: GSE100183	ID: 200100183

2633. Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.
(Submitter supplied) As organisms age, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2544 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81547/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322355
Series		Accession: GSE81547	ID: 200081547

2634. Regulartory effect of HNRNPL and LARP on RNA expression in LNCaP prostate cancer cells
(Submitter supplied) Analysis of RNA expression in LNCaP prostate cancer cells treated with different siRNAs to define the regulatory effect of HNRNPL and LARP on RNA expression.
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/GSE72nnn/GSE72842/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA295183
Series		Accession: GSE72842	ID: 200072842

2635. MCPyV ST activates Max target genes by recruiting TRRAP/EP400 complex
(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 GPL11154 31 Samples
FTP download: GEO (BED, FPKM_TRACKING, TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69878/
Series		Accession: GSE69878	ID: 200069878

2636. EP400 is required for Max and MCPyV mediated gene activation
(Submitter supplied) To determine if EP400 knockdown would affect Max target genes in Merkel cell carcinoma cell line MKL-1, we performed RNA-seq analyses of MKL-1 cells inducibly expressing EP400 shRNA and compared to ChIP-seq data using BETA analyses.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (CSV, FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69876/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA287017
Series		Accession: GSE69876	ID: 200069876

2637. Microarray whole transcriptome profiling of Trichostatin A and Grape Seed Extract in SK-MEL-3 melanoma cells.
(Submitter supplied) In this study, we initially screened over 1400 natural products for capacity to inhibit the kinetic enzyme activity of nuclear HDACs isolated from SK-MEL-3 cells. From these findings we evaluate whole transcriptome changes that occur at a 24 hour time point in SK-ME-3 cells in the presence of a known HDAC inhibitor (Trichostatin A) (1uM) or a natural product HDAC inhibitor Grapeseed Extract (120ug/ml), both tested at sub-lethal concentrations relative to untreated controls. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17692 8 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104265/
Series		Accession: GSE104265	ID: 200104265

2638. Whole transcriptome sequencing data of GBSCC patients from India
(Submitter supplied) Our study has elucidated the immunoregulatory gene expression landscape in primary tumors of Gingivo-Buccal Squamous Cell Carcinoma, as compared to their adjacent normal tissue and computationally estimated a relative composition of various immune cell classes in those tissues. A detailed portrayal of expression variation of immune evasion genes alongwith other potential therapeutic targets have been highlighted in the study.
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/GSE101nnn/GSE101547/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394765
Series		Accession: GSE101547	ID: 200101547

2639. Global modulation of signaling pathways by SARM RAD140 in AR/ER+ breast cancer xenografts
(Submitter supplied) These data demonstrates the regulation of AR and ER pathways by the SARM RAD140 and suggested a unique mechanism of action of RAD140 via the AR-mediated transcription repression.
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/GSE104nnn/GSE104177/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA411985
Series		Accession: GSE104177	ID: 200104177

2640. UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons
(Submitter supplied) The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenotypes is a complex, multilayered process involving both genetics and epigenetics. Parent-of-origin effects of deletion and duplication of the 15q11-q13 locus leading to Angelman, Prader-Willi, and Dup15q syndromes are due to imprinted genes, including UBE3A, which is maternally expressed exclusively in neurons. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL20301 48 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103309/
Series		Accession: GSE103309	ID: 200103309

2641. RNA-seq and small RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line
(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: GPL16791 GPL20301 13 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99900/
Series		Accession: GSE99900	ID: 200099900

2642. RNA-seq analysis of BORIS/CTCFL knockdown in K562 cell line
(Submitter supplied) The study involved transcriptome analysis using RNA-seq knockdown of BORIS/CTCFL gene expression in K652 cancer cell line using inducible shRNA. The K562 cell line is the only cancer cell line that is known to be dependent on BORIS for proliferation and self-renewal of stemness. The goal of the study was to investigate the early/immediate transcriptional response to BORIS downregulation (over 10-fold reduction in protein level) using an inducible shRNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99825/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389734
Series		Accession: GSE99825	ID: 200099825

2643. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters
(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 GPL18573 78 Samples
FTP download: GEO (BED, BROADPEAK, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90634/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352986
Series		Accession: GSE90634	ID: 200090634

2644. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters [RNA-Seq]
(Submitter supplied) BAF complex perturbations contribute to over 20% of human cancer, yet the mechanisms by which these alterations drive oncogenesis remain poorly understood. The driving role for BAF complex mutations in cancer was first documented in malignant rhabdoid tumor (MRT), an aggressive pediatric cancer in which loss of SMARCB1 (also known as BAF47, INI1, hSNF5), a core BAF complex subunit, is the hallmark genetic alteration. 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/GSE90nnn/GSE90633/
Series		Accession: GSE90633	ID: 200090633

2645. Transcriptome profiling of ER+ breast cancer primary tumor and its tumorsphere derivative
(Submitter supplied) We profiled RNA expression in the ER+ primary tumor and the matching tumorspheres. The objective was to find genes differentially expressed between the tumorspheres and bulk tumor.
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/GSE84nnn/GSE84054/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA327871
Series		Accession: GSE84054	ID: 200084054

2646. Genome-wide analysis of YAP and TFCP2 occupancy and regulated expression in liver 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
Platform: GPL20795 18 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99315/
Series		Accession: GSE99315	ID: 200099315

2647. Genome-wide analysis of YAP and TFCP2 down-regulated genes in liver cancer cells
(Submitter supplied) To identify YAP and TFCP2 co-regulated genes, RNA-seq was also performed in Bel-7402 cells before and after knocking down YAP or TFCP2. From the RNA-seq data, 2165 genes were found that were possibly co-regulated by YAP and TFCP2.
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/GSE99nnn/GSE99313/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388096
Series		Accession: GSE99313	ID: 200099313

2648. Genome-wide maps of H3K4me3 and H3K27me3 in SATB1-depleted breast cancer cells
(Submitter supplied) We used chromatin immunoprecipitation-coupled to deep sequencing (ChIP-seq) to profile genome-wide locations of H3K4 trimethylation (H3K4me3) and H3K27 trimethylation (H3K27me3) epigenetic marks in SATB1-depleted MDA-MB-231 aggressive breast cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (BEDGRAPH, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87169/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343775
Series		Accession: GSE87169	ID: 200087169

2649. RNAseq of T-ALL upon long non coding rna purturbation
(Submitter supplied) T cell leukemia cell lines transciptome changes upon long non coding RNA knockdown by CRISPR and ASO. The target lncRNA is a novel lncRNA called "lnrCXCR4". The sequence of this lncRNA is available at the foot of this page.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (PDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104018/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407957
Series		Accession: GSE104018	ID: 200104018

2650. RNA seq_A375 gSMARCB1 +  A549 etoposide, Aurora kinases inhibitors treated
(Submitter supplied) To study the senescence gene signatures in the cells, which were  genetic SMARCB1 depleted or treated with aurora kinase inhibitors or etoposide, we performed next generation RNA sequencing on these cell, and 'FRIDMAN_SENESCENCE_UP' geneset was used to determine the enrichment of senescence-related genes. The RNA sequencing results include (1) A375 cells and SMARCB1 depleted counterparts. (2) A549 cells and aurora kinase inhibitor (Alisertib, barasertib or tozasertib) or etoposide treated counterparts.
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/GSE102nnn/GSE102639/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398256
Series		Accession: GSE102639	ID: 200102639

2651. Impeding transcription of expanded microsatellite repeats by deactivated Cas9
(Submitter supplied) Transcription of expanded microsatellite repeats is associated with multiple human diseases, including myotonic dystrophy, Fuchs’ endothelial corneal dystrophy, and C9orf72-ALS/FTD. Eliminating or reducing production of RNA and proteins arising from these expanded loci holds therapeutic benefit. Here, we tested the hypothesis that a deactivated form of the Cas9 enzyme impedes transcription across expanded microsatellites. 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/GSE103nnn/GSE103997/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407928
Series		Accession: GSE103997	ID: 200103997

2652. The expression of genes encoding palmitoylated proteins in axonal and synaptic compartments is affected in CLN1/PPT1 transfected neuronal cells
(Submitter supplied) CLN1 disease (OMIM #256730) is an early childhood ceroid-lipofuscinosis associated with mutated CLN1, whose product (PPT1) is a lysosomal enzyme involved in the removal of palmitate residues from S-acylated proteins. In neurons, PPT1 is also related to specific functions in the synaptic compartment. The aim of this study was to recognize molecular signatures and functional modules connected with CLN1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15433 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98834/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386335
Series		Accession: GSE98834	ID: 200098834

2653. Mitotic Transcription and Waves of Gene Reactivation During Mitotic Exit
(Submitter supplied) The genome is thought to be transcriptionally silent during mitosis. Technical limitations have prevented the sensitive mapping of mitotic transcription and transcription reactivation during mitotic exit, and thus the networks by which transcriptome dynamics govern the generation of daughter cells have been unclear. We used 5-ethynyluridine to pulse-label intact transcripts during mitosis and mitotic exit and find that the first round of transcription activates genes that are involved in macromolecular synthesis, rather than cell identity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 32 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344882
Series		Accession: GSE87476	ID: 200087476

2654. Comparison of gene expression profiles between SCD1 knockdown and vector control of Huh7 cells and PLC/PRF/5 cells by RNA-sequencing
(Submitter supplied) The purpose of this experiment is to search for the downstream target of SCD1
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/GSE86nnn/GSE86602/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342348
Series		Accession: GSE86602	ID: 200086602

2655. Human tissue-resident memory T cells are defined by core transcriptional and functional signatures in lymphoid and mucosal sites
(Submitter supplied) Tissue resident memory T cells (TRM) mediate optimal protection to site-specific pathogens in mouse models and are key targets for vaccines. In humans, the existence and defining properties of Positive remain unclear. Here, we performed in-depth transcriptome profiling and phenotypic and functional analyses of circulating and resident memory CD4+ and CD8+T cells from lungs, spleens, blood and intestines of 72 individuals, revealing a core gene set conserved between tissues, species, and T cell lineages. 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/GSE94nnn/GSE94964/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374963
Series		Accession: GSE94964	ID: 200094964

2656. miCLIP, RNA-Seq, and Ribo-Seq in MOLM13 cells
(Submitter supplied) We studied the following conditions: m6A RNA methylation in MOLM13 AML cells; METTL3 deficiency on gene expression and translational efficiency
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 21 Samples
FTP download: GEO (BED, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98623/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385767
Series		Accession: GSE98623	ID: 200098623

2657. Episomal S/MAR-based replicons do not alter expression profile of host genome
(Submitter supplied) Methods: mRNA profiles of untransfected HeLa cells (wild-type; wt) were compared with mRNA profiles of HeLa cells stably maintaining an S/MAR-based episome. Results: We here report for the first time that episomally maintained S/MAR-based vectors do not alter gene expression profile of the host cell's genome. No global changes in gene expression in episome maintaining cells, compared to non-transfected cells could be observed. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 2 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97725/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382731
Series		Accession: GSE97725	ID: 200097725

2658. Therapeutic utility of natural estrogen receptor beta agonists on ovarian cancer
(Submitter supplied) We examined the transcriptional changes modulated by ESR2 agonist liquiritigenin by perfroming global transcriptome analysis. ES2 cells were treated with either vehicle or liquiritigenin for 24 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that liquiritigenin modulated several genes that are involved in NF-kB signaling, inflammation, NRF2 mediated oxidative stress response, and MMP signaling.
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/GSE93nnn/GSE93807/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362462
Series		Accession: GSE93807	ID: 200093807

2659. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [NET-seq]
(Submitter supplied) Cancer arises from the malignant interplay between oncogenic signaling and cell specification.  Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry.  To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains.  Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL18573 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79271/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315415
Series		Accession: GSE79271	ID: 200079271

2660. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment [RNA-seq]
(Submitter supplied) Cancer arises from the malignant interplay between oncogenic signaling and cell specification.  Transcriptionally activated stem, growth and survival programs reshape an epigenomic identity defined by a transcriptional core regulatory circuitry.  To study and disrupt oncogenic transcription, we first created inhibitors of BET bromodomains.  Selective antagonism of oncogenic transcriptional signaling arises from bromodomain-specific activity. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 35 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79253/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315414
Series		Accession: GSE79253	ID: 200079253

2661. RNA-seq analysis of the effects of BCL6-inhibiting and BCL6-degrading compounds in lymphoma cell lines
(Submitter supplied) The goal of this experiment is to measure the changes in gene expression induced by small molecules that either inhibit the interaction of the transcription factor BCL6 with co-repressor proteins, or that induce degradation of BCL6, in lymphoma cell lines.
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/GSE94nnn/GSE94099/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA368848
Series		Accession: GSE94099	ID: 200094099

2662. CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL3.shR6.RNAseq.lg]
(Submitter supplied) The death receptor CD95/Fas can be activated by immune cells to kill cancer cells. However, most siRNAs or shRNAs targeting either CD95 or CD95L induce DICE (Death Induced by CD95/CD95L Elimination), a form of cell death in which a combination of different cell death pathways are activated, that is selective for transformed cells, and that preferentially affects cancer stem cells. We now provide evidence that both CD95 and CD95L are part of a network of genes that contain sequences that when expressed as either siRNAs or shRNAs are toxic to cancer cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101234/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393938
Series		Accession: GSE101234	ID: 200101234

2663. CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [FasLRNAseq.lg]
(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/GSE101nnn/GSE101232/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393897
Series		Accession: GSE101232	ID: 200101232

2664. CD95L derived si- and shRNAs and the CD95L mRNA kill cancer cells through an RNAi mechanism by targeting survival genes [siL3.RNAseq.lg]
(Submitter supplied) We provide evidence that shRNAs and siRNAs derived from CD95 and CD95L preferentially target the 3' UTRs of survival genes culminating in a very robust mode of cell death we call DISE (Death Induced by Survival gene Elimination)
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/GSE101nnn/GSE101167/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393831
Series		Accession: GSE101167	ID: 200101167

2665. CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes [shL1.RNAseq.lg]
(Submitter supplied) We provide evidence that shRNAs and siRNAs derived from CD95 and CD95L preferentially target the 3' UTRs of survival genes culminating in a very robust mode of cell death we call DISE (Death Induced by Survival gene Elimination)
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/GSE101nnn/GSE101157/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393824
Series		Accession: GSE101157	ID: 200101157

2666. CD95L derived si- and shRNAs kill cancer cells through an RNAi mechanism by targeting survival genes
(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: GPL20301 56 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87817/
Series		Accession: GSE87817	ID: 200087817

2667. The CCR4-Not complex is a tumor suppressor in Drosophila melanogaster eye cancer models
(Submitter supplied) The CNOT3 protein is a subunit of the CCR4-Not complex, a cytoplasmic protein complex mediating mRNA deadenylation as the first step in mRNA degradation. We recently identified CNOT3 loss-of-function mutations in patients with T-cell acute lymphoblastic leukemia (T-ALL). However, it is not clear yet how loss of this gene is involved in cancer development. Here we use different Drosophila melanogaster eye cancer models to study the potential tumor suppressor function of Not3, the CNOT3 orthologue, as well as other members of the CCR4-NOT complex. more...
Organism:	Homo sapiens; Drosophila melanogaster
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17275 GPL16791 63 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103872/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407359
Series		Accession: GSE103872	ID: 200103872

2668. Gene expression in control and DOCK8 CRISPR KHYG1 NK cells
(Submitter supplied) Mutations in the DOCK8 gene cause an autosomal recessive form of hyper-immunoglobulin E syndrome, characterised by chronic immunodeficiency with persistent microbial infection and increased incidence of malignancy. These manifestations suggest a defect in cytotoxic lymphocyte function and immune surveillance. However, how DOCK8 regulates NK cell-driven immune responses remains unclear. Here, we demonstrate that DOCK8 regulates NK cell cytotoxicity and cytokine production in response to target cell engagement or receptor ligation. 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/GSE101nnn/GSE101467/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394516
Series		Accession: GSE101467	ID: 200101467

2669. Inhibition of the oncogenic fusion protein EWS-FLI1 causes G2/M cell cycle arrest and enhanced vincristine sensitivity in Ewing sarcoma
(Submitter supplied) A chimeric fusion between the RNA binding protein EWS and the ETS family transcription factor FLI1 (EWS-FLI1), created from a chromosomal translocation, is implicated in driving the majority of Ewing sarcomas (ES) by modulation of transcription and alternative splicing. The small molecule YK-4-279 inhibits EWS-FLI1 function and induces apoptosis. We tested 69 anti-cancer drugs in combination with YK-4-279 and found that vinca alkaloids exhibited synergy with YK-4-279 in five ES cell lines. 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/GSE103nnn/GSE103837/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407215
Series		Accession: GSE103837	ID: 200103837

2670. RNA sequencing data for 30 bladder cancer cell lines
(Submitter supplied) RNA-sequencing of a panel of urothelial cancer cells. The goal of the study is to examine the genome-wide expression profile in each of the 30 urothelial cancer cells tested in our laboratory.
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/GSE97nnn/GSE97768/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382834
Series		Accession: GSE97768	ID: 200097768

2671. Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways
(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; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 15 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97018/
Series		Accession: GSE97018	ID: 200097018

2672. Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [RNA-seq]
(Submitter supplied) Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci with hmC-seal was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97003/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380392
Series		Accession: GSE97003	ID: 200097003

2673. Mycobacterium bovis Bacillus Calmette-Guerin (BCG) reprograms melanoma microenvironment to promote antitumor T cell responses
(Submitter supplied) Intralesional therapy using Mycobacterium bovis Bacillus Calmette-Guérin (BCG) for cutaneous metastatic melanoma induces regression of injected, but also non-injected lesions. Tumor-associated macrophages (also known as M2) infiltrate solid tumors and impair antitumor immunity. Since macrophages play a pivotal role in both tumors and mycobacterial infections, we hypothesized BCG alters M2 to promote antitumor immunity. more...
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/GSE90nnn/GSE90748/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355844
Series		Accession: GSE90748	ID: 200090748

2674. ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence
(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 29 Samples
FTP download: GEO (BW, NARROWPEAK) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74621/
Series		Accession: GSE74621	ID: 200074621

2675. ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence [RNA-Seq]
(Submitter supplied) Senescence is a state of stable cell cycle exit that has important implications for development, physiology and disease.  It is distinct from quiescence in which cells can be induced to re-enter the cell cycle. Although it is well known that there are massive changes in the heterochromatin of senescent cells, the molecular mechanisms underpinning the transition from reversible quiescence into irreversible senescence have remained elusive. 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/GSE74nnn/GSE74620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301012
Series		Accession: GSE74620	ID: 200074620

2676. Expression changes in MAPKi resistant M229 melanoma lines co-cultured with PD-1 overexpressing HEK293T cells [CellLine.FPKM.batch5]
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 16 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103711/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA406732
Series		Accession: GSE103711	ID: 200103711

2677. Expression changes in melanoma cell lines under BRAFi treatment timepoints [RNA-Seq.CellLine.batch3]
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103688/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA404058
Series		Accession: GSE103688	ID: 200103688

2678. Expression changes in melanoma cell lines under BRAFi treatment timepoints [RNA-Seq.CellLine.batch4]
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 8 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA404059
Series		Accession: GSE103687	ID: 200103687

2679. RNA-Seq of SHEP TET21N cells upon Doxorubicin treatment
(Submitter supplied) MYCN-high and MYCN-low neuroblastoma cells differ in their responses to Doxorubicin treatment. To explain this difference we compared the global trancriptomes of MYCN-high and MYCN-low cells before, during and after treatment.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 19 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98274/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384515
Series		Accession: GSE98274	ID: 200098274

2680. Cell-cycle-resolved analysis of RNA expression in neuroblastoma cells upon MYCN knockdown
(Submitter supplied) Previous studies of c-MYC or MYCN effects on the cellular transcriptome have been performed with unsynchronized tumor cell populations. We reasoned that these results might have been influenced by different cell-cycle profiles of cells with high or low MYC levels  as the expression of a large part of the genome varies with cell-cycle phase. To correct for this potentially confounding effect, we performed RNA sequencing in cell-cycle-synchronized neuroblastoma cells and then compared the transcriptomes of cells with high and low MYCN in equivalent cell-cycle phases.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 44 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97774/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383104
Series		Accession: GSE97774	ID: 200097774

2681. Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
(Submitter supplied) In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of androgen receptor (AR) blockade by the glucocorticoid receptor (GR). In contrast to fixed genomic alterations, here we show that GR-mediated antiandrogen resistance is adaptive and reversible due to regulation of GR expression by a tissue-specific enhancer. GR expression is silenced in prostate cancer by a combination of AR binding and EZH2-mediated repression at the GR locus, but is restored in advanced prostate cancers upon reversion of both repressive signals. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 41 Samples
FTP download: GEO (TDF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103449/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401755
Series		Accession: GSE103449	ID: 200103449

2682. Autocrine BMP-4 signaling promotes survival of colorectal cancer cells.
(Submitter supplied) Prognoses are poor for colorectal cancer (CRC) patients with metastatic lesions, leading to high demand for the development of novel molecular target therapies. Here, we demonstrate that expression of bone morphogenetic protein 4 (BMP4) is universally up-regulated and endogenous BMP signaling is activated in human CRC cells and tissues. Inhibition of endogenous BMP signaling by the BMP type I receptor inhibitor LDN-193189 led to elevated expression of dual specificity phosphatase 5 (DUSP5) in CRC cells, inducing apoptosis through the dephosphorylation of Erk MAP kinase. 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/GSE96nnn/GSE96914/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380084
Series		Accession: GSE96914	ID: 200096914

2683. RNA-seq analysis of FET cells treated with RSPO1 or TGFβ1
(Submitter supplied) To determine whether RSPO1 and TGFβ1 activate similar transcription, RNA-seq analysis was performed to compare gene profiles after treatment by RSPO1 or TGFβ1. FET cells were treated with RSPO1 or TGFβ1 in triplicates for 4 hours and RNAs extracted from these cells were used for RNA-seq analysis. When gene expression profiles were compared, it was found that 153 genes were commonly regulated by either RSPO1 or TGFβ1. 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/GSE103nnn/GSE103650/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA403844
Series		Accession: GSE103650	ID: 200103650

2684. Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment (RNA-seq_Patient.batch3)
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103658/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA403850
Series		Accession: GSE103658	ID: 200103658

2685. Expression changes in melanoma cell lines pre MAPKi treatment vs. post-MAPKi resistance (RNA-seq_CellLine.batch2)
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
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/GSE103nnn/GSE103630/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA403816
Series		Accession: GSE103630	ID: 200103630

2686. RNA-seq in endometrial stromal tumors
(Submitter supplied) We describe the first analysis of gene expression in endometrial stromal tumors by RNA-seq. We demonstrate that undifferentiated uterine sarcomas have a unique gene expression profile that is distinct from other uterine mesenchymal tumors.
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/GSE87nnn/GSE87581/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345236
Series		Accession: GSE87581	ID: 200087581

2687. Proteogenomic Reveals Biomarkers and Therapeutic Targets in Lymphoid Cancer
(Submitter supplied) Here we find the transcriptional network regulated by ALK oncogenic activitiy in two Anaplastic Large Cell Lymphoma cell lines.
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/GSE81301/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321212
Series		Accession: GSE81301	ID: 200081301

2688. Silencing of Retrotransposons by SETDB1 Inhibits the Interferon Response in Acute Myeloid Leukemia: Data for CRISPR Screen, ChIP-seq, RNA-seq, and Stranded RNA-seq in THP-1 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; Other
Platforms: GPL16791 GPL15520 42 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103411/
Series		Accession: GSE103411	ID: 200103411

2689. RNAseq to determine whether bidirectional transcription occurs over transposable elements following depletion of SETDB1 in THP-1 AML Cells
(Submitter supplied) SETDB1 disruption leads to an increase in the expression of transposable elements as determined by our standard RNAseq, where bidirectional transcription has been reported. We repeated RNA seq on our samples with a stranded prep to determine whether bidirectional transcription occurs of transposable elements following depletion of SETDB1 in THP-1 AML Cells Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103410/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401800
Series		Accession: GSE103410	ID: 200103410

2690. RNAseq to determine gene expression changes following depletion of SETDB1 in THP-1 AML Cells
(Submitter supplied) Purpose: To determine how loss of SETDB1 effects gene expression in THP-1 AML cells.  Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits.  Results: Using an optimized data analysis workflow, we mapped 23 million or more sequence reads per sample to the human genome (GRCh38) with GSNAP for obtaining standard gene expression measurements. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 18 Samples
FTP download: GEO (XLS, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103409/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA401801
Series		Accession: GSE103409	ID: 200103409

2691. Novel KDM1A inhibitors induce differentiation and apoptosis of glioma stem cells via unfolded protein response (UPR) pathway
(Submitter supplied) We examined the transcriptional changes modulated by KDM1A inhibitor NCD-38 by performing global transcriptome analysis. Glioma Stem Cells (GSC10) were treated with either vehicle or NCD-38 for 24 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that NCD-38 modulated several genes that are involved in unfolded protein response, endoplasmic reticulum stress pathway and NRF-2 mediated oxidative stress response.
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/GSE84nnn/GSE84603/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330614
Series		Accession: GSE84603	ID: 200084603

2692. Next Generation Sequencing Transcriptomes of breast cancer
(Submitter supplied) We performed high throughput transcriptome of breast cancer and normal tissues, identifying lincRNA associated molecular subtype with powerful capacity to distinct breast cancer population and predict prognosis. We also identified subtype-specific lincRNAs that may be a useful complement to intrinsic molecular subtype classification when divergence emerges among pathologists.Paired-end transcriptome sequencing were carried out on a cohort of 33 breast tissues from 11 groups including five breast cancer subtypes including luminal A (LA), luminal B (HER2 negative)(LB, HER2-), luminal B (HER2 positive) (LB, HER2+), HER2 and tripple negative breast cancer (TNB), adjacent noncancerous breast tissue (ANT, three samples for each subtype) and the complete normal breast tissues (three samples)
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9115 33 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292118
Series		Accession: GSE71651	ID: 200071651

2693. Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment
(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
4 related Platforms 104 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75313/
Series		Accession: GSE75313	ID: 200075313

2694. Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment (RNA-seq)
(Submitter supplied) Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination with a MEKi typically elicits partial responses. We compared the transcriptomes of patient-derived tumors regressing on MAPKi therapy against MAPKi-induced temporal transcriptomic states in human melanoma cell lines or murine melanoma in immune-competent mice. Despite heterogeneous dynamics of clinical tumor regression, residual tumors displayed highly recurrent transcriptomic alterations and enriched processes, which were also observed in MAPKi-selected cell lines (implying tumor cell-intrinsic reprogramming) or in bulk mouse tumors (and the CD45-negative or -positive fractions,, implying tumor cell-intrinsic or stromal/immune alterations, respectively). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 46 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA303170
Series		Accession: GSE75299	ID: 200075299

2695. Amplification of mutant BRCA2 gene confers resistance to PARP inhibitor
(Submitter supplied) Breast cancer gene 2 (BRCA2) deleterious mutations confer sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition due to its critical role in DNA repair.   PARP inhibitor Olaparib is now approved and several other PARP inhibitors are now in different stages of clinical trials.  Development of resistance to PARP inhibitors limits their clinical utility.  The mechanism of resistance remains not fully understood. 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/GSE86nnn/GSE86394/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA341678
Series		Accession: GSE86394	ID: 200086394

2696. Probing the Roles of SUMOylation in Cancer Cell Biology Using a Selective SAE inhibitor
(Submitter supplied) Small ubiquitin-like modifier (SUMO) family proteins regulate target protein functions by post-translational modification. However, a potent and selective inhibitor to target the SUMO pathway has been lacking.  Here we describe ML-792, the first mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, which leads to reduced cancer cell proliferation. 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/GSE100nnn/GSE100408/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391584
Series		Accession: GSE100408	ID: 200100408

2697. Simultaneous detection and relative quantification of coding and non-coding RNA using a single sequencing reaction
(Submitter supplied) The ability to compare the abundance of one RNA molecule to another is a crucial step for understanding how gene expression is modulated to shape the transcriptome landscape. However, little information is available about the relative expression of the different classes of coding and non-coding RNA or even between RNA of the same class. In this study, we present a complete portrait of the human transcriptome that depicts the relationship of all classes of non-ribosomal RNA longer than sixty nucleotides. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL18573 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99065/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387170
Series		Accession: GSE99065	ID: 200099065

2698. PAF1 regulation of promoter-proximal pause release via enhancer activation
(Submitter supplied) Gene expression in metazoans is regulated by RNA Polymerase II (Pol II) promoter-proximal pausing and its release. Previously, we identified that Pol II-associated factor 1 (PAF1) modulates the release of paused Pol II into productive elongation. Here, we find that PAF1 occupies transcriptional enhancers and restrains hyperactivation of a subset of these enhancers. Enhancer activation as the result of Paf1 loss releases Pol II from paused promoters of nearby PAF1 target genes. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platform: GPL18573 123 Samples
FTP download: GEO (BEDGRAPH, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97527/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382164
Series		Accession: GSE97527	ID: 200097527

2699. Genetic-to-epigenetic Therapy for Pancreatic Cancer
(Submitter supplied) We utilized RNA-Seq to define molecular markers for the effect of chaetocin and MLN8237 combination. PDAC cells were treated with individual drugs or their combination and compared to vehicle. Treatment was limited to 24 hours to extract RNA before significant mitotic catastrophe occurred to capture the transcriptional effect.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97215/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380996
Series		Accession: GSE97215	ID: 200097215

2700. Development of a selective CDK9 degrader from a multi-targeted CDK inhibitor
(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 21 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89386/
Series		Accession: GSE89386	ID: 200089386

2701. Development of a selective CDK9 degrader from a multi-targeted CDK inhibitor [RNA-seq]
(Submitter supplied) Cyclin dependent kinase 9 (CDK9), a key regulator of transcriptional elongation, has long been considered a promising target for cancer therapy, particularly for cancers driven by transcriptional dysregulation.  However, despite promising early clinical data in blood cancers using pan-CDK inhibitors that potently inhibit CDK9 such as Dinaciclib and Flavopiridol, no selective CDK9 inhibitors have been clinically approved. 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/GSE89nnn/GSE89385/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352098
Series		Accession: GSE89385	ID: 200089385

2702. Distinct changes in transcriptional profiles and epigenetic patterns mediated by EZH2 inhibitors in sensitive and insensitive prostate cancer 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
Platforms: GPL11154 GPL18573 21 Samples
FTP download: GEO (BED, BROADPEAK, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80240/
Series		Accession: GSE80240	ID: 200080240

2703. EZH2 inhibitor-mediated transcriptional profiling in prostate cancer cells [RNA-seq]
(Submitter supplied) We reported here the gene expression profiles that were mediated upon the treatment of EZH2 inhibitor in two hormone-refractory prostate cancer cell lines: the sensitive, AR-positive abl cells and the insensitive, AR-null DU145 cells.
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/GSE80nnn/GSE80239/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318380
Series		Accession: GSE80239	ID: 200080239

2704. Gene expression profile using RNA-seq in WC00060 or SR-0788 cells transfected with siRNA for KPC1 or control
(Submitter supplied) Melanoma is a highly aggressive cancer with increasing incidence rates and a poor survival, particularly in patients with AJCC stage IV and advanced stage III. Deregulation of NF-kB is linked to different pathological states, including melanoma. To identify the involvement of NF-kB pathway regulation in melanoma progression, we manipulated NF-kB pathway activation and profiled gene expression using RNA-sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 8 Samples
FTP download: GEO (CSV, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79112/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314973
Series		Accession: GSE79112	ID: 200079112

2705. Transcriptome analysis by RNA-seq of ovarian cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.
(Submitter supplied) We performed the RNA-seq experiments for mRNA of ovarian cancer tissue. Raw data not provided. Institutional Review Board (IRB) does not allow submitters to disclose raw data to the public
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 58 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101948/
Series		Accession: GSE101948	ID: 200101948

2706. FOXP2's impact on the primate transcriptome
(Submitter supplied) The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In spite of its relevance, the FOXP2-controlled network and its functional implications are only partially understood. Therefore, we analyzed the transcriptomes of human neuroblastoma cells (SH-SY5Y) stably overexpressing human, chimpanzee, macaque, and marmoset FOXP2 cDNAs. Clones carrying empty vector served as a standard of baseline expression. 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/GSE100nnn/GSE100291/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391264
Series		Accession: GSE100291	ID: 200100291

2707. Gene expression in GBM with Cav3.2 inhibition
(Submitter supplied) Glioblastoma stem cells (GSCs) have been implicated in tumor initiation, progression and resistance to therapy. We investigated the expression, function, mechanisms of action and therapeutic targeting of T-type calcium channels (Cav3.2) with the FDA approved and repurposed drug mibefradil in glioblastoma (GBM), and GSCs. We found that Cav3.2 is highly expressed in human GBM specimens and enriched in GCSs. 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/GSE95nnn/GSE95106/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376103
Series		Accession: GSE95106	ID: 200095106

2708. Akt Activation Mediates Acquired Resistance to Fibroblast Growth Factor Receptor Inhibitor BGJ398
(Submitter supplied) Activation of fibroblast growth factor receptor (FGFR) signaling through mutations, amplifications, or fusions involving FGFR1, 2, 3, or 4 are seen in multiple tumors including lung, bladder, and cholangiocarcinoma. Currently, several clinical trials are evaluating the role of novel FGFR inhibitors in solid tumors. As we move forward with FGFR inhibitors clinically, we anticipate emergence of resistance with treatment. 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/GSE92nnn/GSE92651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358239
Series		Accession: GSE92651	ID: 200092651

2709. Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture
(Submitter supplied) We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p<0.01) between CC-CR and CC; there were 141 transcripts upregulated and 220 transcripts downregulated in CC-CR compared to CC. Small RNA-Seq detected 7 miRNAs upregulated and 24 miRNAs downregulated in CC-CR cells compared to CC cells (fold change>2, FDR<0.01). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82236/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324412
Series		Accession: GSE82236	ID: 200082236

2710. RNA-Chromatin Interactome Reveals Enhancer-Promoter Connectivity in 3D Genome
(Submitter supplied) High eukaryotic genomes are populated with enhancers, but it has been a major challenge in defining specific enhancer-promoter relationship. Enhancers can also be divided into typical and super-enhancers, yet their functional distinctions remain to be understood. Here, we report a strategy to capture in situ Global RNA Interactions with DNA by deep sequencing (GRID-seq). By deducing general RNA background on chromatin, we unexpectedly detect a highly selective set of RNAs (including both lncRNAs and protein-coding pre-mRNAs) decorated on enhancers, particularly super-enhancers. more...
Organism:	Drosophila melanogaster; Homo sapiens; Mus musculus
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL17275 GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82312/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324602
Series		Accession: GSE82312	ID: 200082312

2711. Neuronal activity promotes glioma growth
(Submitter supplied) Secreted molecules from active neurons promote glioma growth
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/GSE62nnn/GSE62563/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA264418
Series		Accession: GSE62563	ID: 200062563

2712. Effect of Hypoxia in Severe Preeclampsia through Epigenetic Regulation
(Submitter supplied) Though the pathophysiology of preeclampsia (PE) is unclear worldwide, placental hypoxia has been implicated in the pathologic processes of PE.In this study, we profiled the transcriptome in BeWo and JEG-3 cells cultured in hypoxic condition or normal ones based on the RNA sequencing dataset. After filtered the low-quality ones, the RNA readers was aligned to human genome hg19 by TopHat and then assembled by Cufflinks. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72437/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294057
Series		Accession: GSE72437	ID: 200072437

2713. RNA-seq analysis of melanoma and carcinoma cells expressing FOXQ1
(Submitter supplied) We report the genome wide RNA sequencing for high-throughput profiling of FOXQ1 target genes in melanoma and carcinoma cells. We generated melanoma (SK-Mel-147) and ovarian carcinoma cells (SCOV3) ectopically expressing FOXQ1. We find that FOXQ1 differentially regulates the expression of several genes in melanoma cells as compared to carcinoma cells. Specifically, FOXQ1 induces the expression of several genes in ovarian carcinoma cells SCOV3 and suppresses the expression of the same genes in melanom 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/GSE103nnn/GSE103071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA400078
Series		Accession: GSE103071	ID: 200103071

2714. TAp73 is a marker of glutamine addiction in medulloblastoma
(Submitter supplied) Metabolically-targeted therapies hold the promise of offering an effective and less toxic treatment for tumours including medulloblastoma, the most common malignant brain tumour of childhood. Current treatment relies on the sensitivity of these tumours to DNA damage that was discovered more than 50 years ago. Finding new tumour-specific susceptibilities to complement sensitivity to DNA damage is key to developing new more effective adjuvant therapies. 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/GSE103nnn/GSE103029/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399844
Series		Accession: GSE103029	ID: 200103029

2715. O-GlcNAc expression levels epigenetically regulate colon cancer tumorigenesis by affecting the cancer stem cell compartment via modulating expression of transcriptional factor MYBL1
(Submitter supplied) To study the regulation of colorectal adenocarcinoma progression by O-GlcNAc, we have focused on the O-GlcNAc-mediated epigenetic regulation of human colon cancer stem cells (CCSC). Xenograft tumors from colon tumor cells with OGT knockdown grew significantly slower than those formed from control cells, indicating a reduced proliferation of tumor cells due to inhibition of OGT expression. Significant reduction of CCSC population was observed in the tumor cells after OGT knockdown, while tumor cells treated with O-GlcNAcase inhibitor showed an increased CCSC population, indicating that O-GlcNAc levels regulated the CCSC compartment. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93656/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361479
Series		Accession: GSE93656	ID: 200093656

2716. SBF2-AS1 promotes tumorigenesis as a miRNA sponge in lung cancer
(Submitter supplied) Long noncoding RNA (lncRNA) play important roles in the pathogenesis of cancer. LncRNA SBF2-AS1is unregulated in lung cancer tissues, while its biological function and molecular mechanism are largely unknown. RNA sequencing results suggest cell cycle-related genes are altered after SBF2-AS1 knockdown. In vivo and in vitro experiments confirm SBF2-AS1 could promote tumorigenesis of lung cancer. Further experiments prove SBF2-AS1 could bind with miR-338-3p and miR-362-3p to regulate various cell cycle-related genes, including E2F1. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103016/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399758
Series		Accession: GSE103016	ID: 200103016

2717. Cancer-specific retargeting of BAF complexes by a prion-like domain
(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 85 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94278/
Series		Accession: GSE94278	ID: 200094278

2718. Cancer-specific retargeting of BAF complexes by a prion-like domain [RNA-Seq]
(Submitter supplied) Alterations in the function of transcriptional regulators can orchestrate oncogenic programs that are critical for the transformation and survival of cancer cells. Here we show that the BAF chromatin remodeling complex, which is mutated in over 20% of human tumors, interacts with EWSR1, a member of the FET family of proteins containing prion-like domains that are frequent partners in oncogenic fusions with transcription factors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 29 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369237
Series		Accession: GSE94277	ID: 200094277

2719. Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression
(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 90 Samples
FTP download: GEO (IDAT, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102996/
Series		Accession: GSE102996	ID: 200102996

2720. Glioblastoma stem cells infected by ZIKA virus
(Submitter supplied) We repoted the Glioblastoma stem cells(GSCs) infected by two strains of ZIKA virus, the Brazil and Dakar strains. The ZIKV was added into the medium of GSCs for 48 hours, the RNA was harvested after ZIKV infection. We found that the GSCs up-regulated the Type 1&2 interferons after infected by ZIKV
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102924/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399336
Series		Accession: GSE102924	ID: 200102924

2721. Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles
(Submitter supplied) We have investigated the genomic and epigenetic consequences of co-culturing colorectal carcinoma cells with membrane vesicles from pathogenic bacteria Vibrio cholerae and non-pathogenic commensal bacteria Escherichia coli. Our study has revealed that membrane vesicles from pathogenic and commensal bacteria have a global impact on the gene expression of coloncarcinoma cells. The changes in gene expression correlated positively with both epigenetic changes and chromatin accessibility of promoters at transcription start sites of genes induced by both types of membrane vesicles. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102923/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399284
Series		Accession: GSE102923	ID: 200102923

2722. Zika Virus Has Oncolytic Activity against Glioblastoma Stem Cells
(Submitter supplied) We explored the utility of oncolytic virus therapy against glioblastoma with Zika virus (ZIKV), a flavivirus that induces cell death and differentiation of neural precursor cells in the developing fetus. ZIKV preferentially infected and killed glioblastoma stem cells (GSCs) relative to differentiated tumor progeny or normal neuronal cells. The effects against GSCs were not a general property of neurotropic flaviviruses, as West Nile Virus (WNV) indiscriminately killed both tumor and normal neural 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/GSE102nnn/GSE102244/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397077
Series		Accession: GSE102244	ID: 200102244

2723. Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-seq C-terminal mutant]
(Submitter supplied) Targeting the activation function-1 (AF-1) at the N-terminus of the androgen receptor (AR) is an attractive therapeutic alternative to the current approaches to inhibit AR action in prostate cancer (PCa). Here we show that the AR AF-1 is bound by the BAG domain of the cochaperone Bag-1L. Mutations in this domain or loss of Bag-1L abrogates AR signaling and reduces PCa growth. Correspondingly, Bag-1L protein levels increase with progression of primary prostate tumors to castration-resistant PCa, correlating inversely with patient response to abiraterone therapy. 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/GSE102nnn/GSE102183/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396941
Series		Accession: GSE102183	ID: 200102183

2724. Targeting the androgen receptor N-terminus via the cochaperone Bag-1L [RNA-Seq KO]
(Submitter supplied) Targeting the activation function-1 (AF-1) at the N-terminus of the androgen receptor (AR) is an attractive therapeutic alternative to the current approaches to inhibit AR action in prostate cancer (PCa). Here we show that the AR AF-1 is bound by the BAG domain of the cochaperone Bag-1L. Mutations in this domain or loss of Bag-1L abrogates AR signaling and reduces PCa growth. Correspondingly, Bag-1L protein levels increase with progression of primary prostate tumors to castration-resistant PCa, correlating inversely with patient response to abiraterone therapy. more...
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/GSE89nnn/GSE89917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354527
Series		Accession: GSE89917	ID: 200089917

2725. Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Methylation profiling by genome tiling array; Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL13534 GPL571 GPL16791 211 Samples
FTP download: GEO (BEDGRAPH, CEL, IDAT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85942/
Series		Accession: GSE85942	ID: 200085942

2726. Large-Scale Atlas of Mutant IDH1-Dependent Chromatin State Reprogramming, Reversibility, and Persistence [RNA-seq]
(Submitter supplied) Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) mutations drive the development of gliomas and other human malignancies.  Significant efforts are already underway to attempt to target mutant IDH in clinical trials.  However, how mutation of IDH leads to tumorigenesis is poorly understood. Mutant IDH1 promotes epigenetic changes that promote tumorigenesis but the scale of these changes throughout the epigenome and the reversibility of these changes are unknown. more...
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/GSE85nnn/GSE85941/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339799
Series		Accession: GSE85941	ID: 200085941

2727. Sequence dependency and regulatory function of dimeric NOTCH1/RBPJ complexes on coding and non-coding transcription in T-lymphoblastic leukemia
(Submitter supplied) NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expression. The complex can function as monomer and dimer. How dimeric complexes regulate gene expression in human cancer is not well studied. Here, we integrate genomic data sets and analyze Notch dimeric complexes-regulated transcriptome and cis-regulatory elements. A subset of coding and non-coding RNA is Notch dimeric complexes-associated. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72482/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294137
Series		Accession: GSE72482	ID: 200072482

2728. Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs
(Submitter supplied) VHL loss is the most common genetic alteration event in ccRCC, but its effect on epigenetic landscape has not been elucidated previously. We describe the genome-wide cis-regulatory landscapes of VHL-deficient ccRCC tumors by comparing the epigenetic changes in terms of histone modifications (H3K27ac, H3K4me1, H3K4me3)  with the transcriptomics profiles in 10 pairs of normal kidney and ccRCC tissues.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 20 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102101/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396588
Series		Accession: GSE102101	ID: 200102101

2729. Chromatin-associated protein interactions drive megadomain formation in NUT midline carcinoma
(Submitter supplied) To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT-midline carcinoma, we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared to wild type BRD4.  Using crosslinking, affinity purification, and mass spectrometry, we identify the p300 acetyltransferase as ectopically associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (TDF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96775/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379616
Series		Accession: GSE96775	ID: 200096775

2730. JAK dependent survival of ALK- ALCL
(Submitter supplied) Activating JAK and STAT mutations were discovered in many T-cell malignancies including ALK- anaplastic large cell lymphomas (ALCL). However, such mutations often occur in a minority of patients. To investigate the clinical application of targeting Janus Kinase (JAK) for ALK- ALCL, we treated ALK- cell lines of different histologic origins with JAK inhibitors. Interestingly, most exogenous cytokine independent cell lines responded to JAK inhibition regardless of JAK mutation status. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 9 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96048/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378660
Series		Accession: GSE96048	ID: 200096048

2731. BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response
(Submitter supplied) BRCA1 associated protein 1 (BAP1) is a tumor suppressor with de-ubiquitinating (DUB) enzyme activity and has been implicated in chromatin regulation of gene transcription. The goal of this study is to identify BAP1-dependent transcriptional alterations under both basal (25 mM glucose) and glucose starvation (0 mM glucose) conditions. To this end, we established UMRC6 cell lines (a BAP1 deficient renal cancer cell line) stably expressing Flag-tagged BAP1 wild-type (U6-F), and the empty vector control cells (U6-EV), and performed RNA sequencing (RNA-Seq) analysis in U6-EV and U6-F stable cell lines at 0, 4, and 8 hour upon glucose starvation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95097/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376054
Series		Accession: GSE95097	ID: 200095097

2732. Expression level is a key determinant of E2F1-mediated cell fate
(Submitter supplied) Purpose: dose response analysis of E2F1 target genes expression in flow-sorted fractions with increasing amounts of fluorescently labled E2F1 Methods:U2OS pTRIPZ-YFP-ER-E2F1 cells were grown in full serum-containing growth medium and treated with 500 ng/ml doxycycline for 48 hours followed by addition of 90 nM OHT for an additional 20 hours. Cells from different YFP fractions were sorted by flow cytometry. more...
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/GSE93nnn/GSE93365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360815
Series		Accession: GSE93365	ID: 200093365

2733. Identification of a core p53 transcriptional program with highly fractionated tumor suppressive activity
(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: GPL17303 GPL16791 61 Samples
FTP download: GEO (BIGWIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86222/
Series		Accession: GSE86222	ID: 200086222

2734. Total RNA-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin
(Submitter supplied) To determine effects of p53 activation on steady-state mRNA levels, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116 (p53+/+ and p53 -/-), breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 16 Samples
FTP download: GEO (BIGWIG, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86221/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340956
Series		Accession: GSE86221	ID: 200086221

2735. RNAseq from polysomal RNA harvested from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin
(Submitter supplied) To determine effects of p53 activation on levels of RNA associated with polysomes, we performed RNA-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (BIGWIG, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86219/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340954
Series		Accession: GSE86219	ID: 200086219

2736. GRO-seq from HCT116, MCF7 and SJSA cell lines treated with DMSO and Nutlin
(Submitter supplied) To identify loci with transcriptionally engaged RNA polymerase, we performed GRO-seq analysis of colorectal carcinoma cell line HCT116, breast carcinoma line MCF7, and osteosarcoma line SJSA treated with MDM2 inhibitor Nutlin.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (BW, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86165/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA340395
Series		Accession: GSE86165	ID: 200086165

2737. VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell 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
Platforms: GPL11154 GPL16791 195 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86095/
Series		Accession: GSE86095	ID: 200086095

2738. Genomic deletion of malic enzyme 2 confers collateral lethality in pancreas cancer
(Submitter supplied) Comparison of malic enzyme 3 (ME3) depleted vs non-depleted xenograft tumors. ME3 is an isoform of ME2.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80411/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318816
Series		Accession: GSE80411	ID: 200080411

2739. Co-regulation of transcription by BRG1 and Brm, two mutually exclusive SWI/SNF ATPase subunits
(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 53 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102561/
Series		Accession: GSE102561	ID: 200102561

2740. Cooperative and Antagonistic Transcriptional Regulation by BRG/BRM [RNA-seq]
(Submitter supplied) We monitored the transcription changes associated with loss of BRG1, BRM, or both combined I HepG2 cells to understand the functional relationship between two mutually exlusive subunits of SWI/SNF
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/GSE102nnn/GSE102560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398038
Series		Accession: GSE102560	ID: 200102560

2741. Genetic and pharmacological restoration of TET2 function blocks stem cell self-renewal and progression of leukemia
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL16791 GPL17021 80 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97442/
Series		Accession: GSE97442	ID: 200097442

2742. RNA-sequencing of human leukemia cells and mouse hematopoietic progenitors
(Submitter supplied) human leukemia cells treated with vitamin C for 12 and 72hrs and mouse hematopoietic progenitor cells with knockdown and Tet2 restoration
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/GSE97nnn/GSE97440/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381792
Series		Accession: GSE97440	ID: 200097440

2743. Neuroblastoma cells undergo transcriptomic alterations during dissemination into the bone marrow and subsequent tumor progression
(Submitter supplied) Background: Neuroblastoma is the most common extracranial solid tumor in childhood. The vast majority of stage M patients present with disseminated tumor cells (DTCs) in the bone marrow (BM). Although these cells represent a major obstacle in the treatment of neuroblastoma patients, their transcriptomic profile was not intensively analyzed so far. Results: RNA-Seq of stage M primary tumors, enriched BM-derived DTCs and the corresponding non-tumor mononuclear cells (MNCs) revealed that DTCs largely retained the gene expression signature of tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 86 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94035/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA368627
Series		Accession: GSE94035	ID: 200094035

2744. Hypoxic transcriptome of SQ20B human head and neck cancer cells
(Submitter supplied) We have carried out deep directional sequencing of  mRNA isolated from normoxic (control) SQ20B cells (N=4) and hypoxic (16h at 0.5% oxygen) cells (N=4).
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/GSE87nnn/GSE87456/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA344795
Series		Accession: GSE87456	ID: 200087456

2745. Mutant p53 Shapes the Enhancer Landscape of Cancer Cells in Response to Chronic Immune Signaling
(Submitter supplied) We establish a mechanism by which chronic TNF-a signaling orchestrates a functional interplay between mutant p53 and NFkB that underlies altered patterns of cancer promoting gene expression.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
Platform: GPL20301 17 Samples
FTP download: GEO (BIGWIG, CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102796/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA399115
Series		Accession: GSE102796	ID: 200102796

2746. Effect of selective glucocorticoid receptor modulation (SGRM) on gene expression in human prostate cancer cell lines
(Submitter supplied) Human prostate cancer cell lines treated with androgen receptor (AR) agonists/antagonists and concurrent glucocorticoid receptor (GR) agonist/antagonists
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/GSE97nnn/GSE97204/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380950
Series		Accession: GSE97204	ID: 200097204

2747. RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of AIM2.
(Submitter supplied) Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Chronic inflammation has been recognized as a risk factor for cSCC and inflammation is a typical feature of the progression of actinic keratosis lesions to invasive and metastatic cSCC. Inflammasomes are important components of the innate immune response involved in onset of inflammation. 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/GSE94nnn/GSE94270/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369227
Series		Accession: GSE94270	ID: 200094270

2748. 4β-Hydroxywithanolide E Modulates Alternative Splicing of Apoptotic Genes in Human Hepatocellular Carcinoma Huh-7 Cells
(Submitter supplied) Alternative splicing is a mechanism for increasing the protein variety of a limited number of genes. Studies have shown that aberrant regulations of the alternative splicing of apoptotic gene transcripts may contribute to the development of cancer. In this study, we isolated 4β-Hydroxywithanolide E (4bHWE) from the traditional herb Physalis peruviana, and analyzed its biological effects in cancer cells. 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/GSE79nnn/GSE79884/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA317320
Series		Accession: GSE79884	ID: 200079884

2749. Estrogen receptor coregulator binding modulators (ERXs) effectively target estrogen receptor positive human breast cancers
(Submitter supplied) We examined the transcriptional chagnes modulated by ECBI-11 by perfroming global transcriptome analysis. ZR75 cells were treated with either control or ECBI-11 in the presence of E2 for 48 h and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that ECBI modulated several genes that are involved in cell cycle, breast cancer signaling, estrogen signaling and apoptosis.
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/GSE75nnn/GSE75664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA305002
Series		Accession: GSE75664	ID: 200075664

2750. First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor
(Submitter supplied) The polycomb repressive complex 2 (PRC2) histone methyl-transferase plays a central role in epigenetic regulation in development and in cancer, and hence to interrogate its role in a specific developmental transition, methods are needed for disrupting function of the complex with high temporal and spatial precision. The catalytic and substrate recognition functions of PRC2 are coupled by binding of the N-terminal helix of the Ezh2 methylase to an extended groove on the EED trimethyl lysine binding subunit. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (BW, TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102702/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA398471
Series		Accession: GSE102702	ID: 200102702

2751. Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells [RNA-seq]
(Submitter supplied) Human pluripotent stem cells (hPSCs) are an important player in disease modeling and regenerative medicine. Nonetheless, multiple studies uncovered their inherent genetic instability upon prolonged culturing, where specific chromosomal aberrations provide cells with a growth advantage. These positively selected modifications have dramatic effects on multiple cellular characteristics. Epigenetic aberrations also possess the potential of changing gene expression and altering cellular functions. 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/GSE99nnn/GSE99651/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389212
Series		Accession: GSE99651	ID: 200099651

2752. CDK4/6 inhibition and tumor immunity
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17303 GPL18635 45 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99063/
Series		Accession: GSE99063	ID: 200099063

2753. Transcriptomic analysis in PDX mammary carcinoma after CDK4/6 inhibition
(Submitter supplied) We measured changes in expression of 20,812 human genes PDX tumors growing in mice after treatment with abemaciclib
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99062/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387166
Series		Accession: GSE99062	ID: 200099062

2754. Transcriptomic analysis in breast cancer cell lines after CDK4/6 inhibition
(Submitter supplied) We measured changes in expression of 20,812 genes in human breast cancer cell lines after treatment with abemaciclib
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 18 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99060/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387164
Series		Accession: GSE99060	ID: 200099060

2755. Knock-down of Ror1 in MDA-MB-231 cell line decreases cell invasiveness
(Submitter supplied) RNA-Seq profiling of triple-negative MDA-MB-231 cell line with know-down of non-canonical WNT signaling receptor Ror1. The MDA-MB231 cells were either transfected with a non-sense control shRNA (shCTL) or with a ROR1 shRNA (shROR1) construct. The objective was to find expression-responsive targets of these perturbations as potential drivers of MDA-MB231 cell invasiveness.
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/GSE96nnn/GSE96637/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379273
Series		Accession: GSE96637	ID: 200096637

2756. Targets of ROR2 overexpression in MCF-7 cells revealed a differentially regulated module of non-canonical WNT signaling pathway
(Submitter supplied) RNA-Seq profiling of estrogen-receptor-positive MCF-7 cell lines with different perturbations of non-canonical WNT signaling . The MCF-7 cells were either transfected with an empty vector (pcDNA) or with a ROR2 overexpression construct, in parallel with or without stimulation with recombinant WNT5A. The objective was to find expression-responsive targets of these perturbations as potential drivers of increased cell invasiveness.
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/GSE74nnn/GSE74383/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA300208
Series		Accession: GSE74383	ID: 200074383

2757. Swarm intelligence-enhanced detection of non-small cell lung cancer using tumor-educated platelets
(Submitter supplied) We report RNA-sequencing data of 779 blood platelet samples, including 402 tumor-educated platelet (TEP) samples collected from patients with non-small cell lung cancer (NSCLC). In addition, we report RNA-sequencing data of blood platelets isolated from 377 individuals without reported cancer, but not excluding individuals with inflammatory conditions. This dataset highlights the ability of TEP RNA-based 'liquid biopsy' diagnostics in patients with NSCLC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 779 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89843/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353588
Series		Accession: GSE89843	ID: 200089843

2758. AKT activation directs LPA-induced invasion of ovarian cancer cells through HIF1α-ETS-1 axis
(Submitter supplied) We sequenced the global transcriptome of human ovarian cancer cell line treated Vs untreated to identify the pathways and genes that are regulating the metabolite-induced invasion in ovarian cancer cells.
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/GSE87nnn/GSE87087/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343474
Series		Accession: GSE87087	ID: 200087087

2759. The Genomic Landscape of Atypical Fibroxanthoma
(Submitter supplied) In this study, we used exome sequencing and RNA sequencing to describe the genomic landscape of Atypical Fibroxanthoma (AFX). Using exome sequencing data, we identified several genes commonly mutated in our samples such as CSMD3, COL11A1, and FAT1. We also identified deletions in chr9p and chr13q in the AFX tumors. Using our RNA-sequencing data, we identified 8591 differentially expressed genes, of which 3524 genes had at least a 2 log fold change between AFX tumors and normal keratinocytes. 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/GSE85nnn/GSE85671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339046
Series		Accession: GSE85671	ID: 200085671

2760. Gene expression by high-throughput sequencing of T47D-MTVL human breast cancer cells upon H1.4 knock-down and multiple H1 variants
(Submitter supplied) Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (120sh) or multiple H1 variants (225sh)
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/GSE83nnn/GSE83277/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA325483
Series		Accession: GSE83277	ID: 200083277

2761. A germline mutation in SRRM2, a splicing factor gene, is implicated in papillary thyroid carcinoma predisposition
(Submitter supplied) Papillary thyroid carcinoma (PTC) displays strong but so far largely uncharacterized heritability. Here we studied genetic predisposition in a family with six affected individuals. We genotyped all available family members and conducted whole exome sequencing of blood DNA from two affected individuals. Haplotype analysis and other genetic criteria narrowed our list of candidates to a germline variant in the serine/arginine repetitive matrix 2 gene (SRRM2). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL9052 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE68nnn/GSE68058/
Series		Accession: GSE68058	ID: 200068058

2762. Altered expression of genes in lncRNA-LBCS, hnRNPK and PTBP1 knockdown
(Submitter supplied) We identify a lncRNA which low expresses and regulates self-renewal of bladder cancer stem cell. So we named it lncRNA-LBCS (low expresses in bladder cancer stem cell). Further study finds that lncRNA-LBCS bind to hnRNPK and PTBP1. To investigate the genes regulated by these, we knockdown lncRNA-LBCS, hnRNPK and PTBP1 by siRNA, respectively, and perform high-throughput sequence. So we identify a series of genes regulated by lncRNA-LBCS, hnRNPK and PTBP1, respectively.
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/GSE79nnn/GSE79832/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314922
Series		Accession: GSE79832	ID: 200079832

2763. Targeting neuronal activity-regulated neuroligin-3 dependency for high-grade glioma therapy
(Submitter supplied) Neuronal activity promotes high-grade glioma (HGG) growth. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule and glioma mitogen neuroligin-3 (Nlgn3), but the therapeutic potential of targeting Nlgn3 in glioma remains to be defined. We demonstrate a striking dependence of HGG growth on microenvironmental Nlgn3 and determine a targetable mechanism of secretion. 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/GSE99nnn/GSE99045/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387119
Series		Accession: GSE99045	ID: 200099045

2764. Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells
(Submitter supplied) The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LCC9 tamoxifen-resistant breast cancer cell lines relative to parental MCF-7 tamoxifen-sensitive cells
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/GSE81nnn/GSE81620/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322129
Series		Accession: GSE81620	ID: 200081620

2765. Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs with in vivo activity in hematological malignancies
(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: GPL11154 GPL16686 14 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78932/
Series		Accession: GSE78932	ID: 200078932

2766. Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs with in vivo activity in hematological malignancies [RNA-Seq]
(Submitter supplied) The indisputable role of epigenetics in cancer and the fact that epigenetic alterations can be reversed have favored development of epigenetic drugs. In this study, we have designed and synthesized potent novel, selective and reversible chemical probes that simultaneously inhibit the G9a and DNMTs methyltransferase activity. In vitro treatment of hematological neoplasia (Acute Myeloid Leukemia-AML, Acute Lymphoblastic Leukemia-ALL and Diffuse Large B-cell Lymphoma-DLBCL) with the lead compound CM-272, inhibited cell proliferation and promoted apoptosis, inducing interferon stimulated genes and immunogenic cell death. 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/GSE78nnn/GSE78930/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314452
Series		Accession: GSE78930	ID: 200078930

2767. Choline kinase alpha (CHKA) as a therapeutic target in pancreatic ductal adenocarcinoma: Expression, predictive value, and sensitivity to inhibitors
(Submitter supplied) Choline kinase alpha (CHKA) plays a crucial role in the regulation of membrane phospholipid synthesis and has oncogenic properties in vitro. We have analyzed the expression of CHKA in cell lines derived from pancreatic ductal adenocarcinoma (PDAC) and have found increased CHKA expression and a good correlation between protein expression and sensitivity to MN58b, a CHKA inhibitor that reduced cell growth through the induction of apoptosis. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 6 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE60nnn/GSE60321/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA258026
Series		Accession: GSE60321	ID: 200060321

2768. Lack of Repressive Capacity of Human Promoter DNA Methylation identified through Genome-Wide Epigenomic Manipulation
(Submitter supplied) It is widely assumed that the addition of DNA methylation at gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression. The effect of forced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we conducted artificial methylation of thousands of human promoters in human cells using an artificial zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription and histone modifications, and the durability of DNA methylation after the removal of the fusion protein. more...
Organism:	Homo sapiens
Type:		Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL18460 40 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397651
Series		Accession: GSE102395	ID: 200102395

2769. Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]
(Submitter supplied) The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platform: GPL19415 2 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84353/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328978
Series		Accession: GSE84353	ID: 200084353

2770. Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-based Subtypes
(Submitter supplied) We performed an integrated genomic analysis of NPC using a large clinical cohort of treatment-naïve tumor specimens which identified three gene expression-based subtypes differing in their pattern of immune and stromal gene expression.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 113 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102349/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA397538
Series		Accession: GSE102349	ID: 200102349

2771. Gene expression profile in breast cancer cell lines using RNA sequencing
(Submitter supplied) In order to identify novel molecular targets associated with TNBC progression, we initially performed transcriptome analysis using RNA sequencing in breast cancer cell lines, classified as either the luminal subtype (MCF-7, T47D, ZR-75B) or basal-like subtype (MDA-MB-231, MDA-MB-435, Hs578T).
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/GSE100878/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393329
Series		Accession: GSE100878	ID: 200100878

2772. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors [RNA-seq]
(Submitter supplied) Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this is sufficient to drive cellular transformation in the absence of genetic mutations is not clear. To investigate this question, we use a CRISPR/dCas9 based epigenetic editing tool, where an inactive form of Cas9 is fused to DNMT3A and its regulator DNMT3L. Using this system, we show simultaneous de novo DNA methylation of genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN in primary myoepithelial cells isolated from healthy human breast tissue. 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/GSE100nnn/GSE100027/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA390528
Series		Accession: GSE100027	ID: 200100027

2773. High-throughput RNA sequencing on circular RNA profiles of human bladder cancer tissues and normal bladder tissues
(Submitter supplied) In order to find out circular RNAs profiles in human bladder cancer tissues and normal bladder tissues, we characterized circuclar RNA transcripts by performing RNA-Seq on ribosomal RNA-depleted total RNA from three pairs of human bladder cancer tissues and paired normal bladder tissues.A computational pipeline based on the anchor alignment of unmapped reads was used to identify circular RNAs. Collectively, we identified16,535 distict circular RNAs, most of them origined from exons (88.96%), others from introns, linc RNA, intergenic region, 3’UTR and 5’UTR. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 6 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97239/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381054
Series		Accession: GSE97239	ID: 200097239

2774. Effect of FGF13 depletion on the H460 cell line
(Submitter supplied) The purpose of our study was to explore the relevance of the FGF13 protein in a NSCLC cell line
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/GSE102nnn/GSE102185/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396939
Series		Accession: GSE102185	ID: 200102185

2775. Transcriptome analysis of CD133 overexpressed U87MG glioblastoma cells
(Submitter supplied) This study investigated the biological function of CD133 by ectopic expression of CD133 in U87MG cell line. Although CD133 is widely used as a cancer stem cell marker, there are a few studies that examined its own biological functions. While a number of loss-of-function studies about CD133 have shown that CD133 have effects on cancer progression, there are few gain-of-function studies about functions of CD133. 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/GSE99nnn/GSE99385/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388345
Series		Accession: GSE99385	ID: 200099385

2776. Measuring the effect of MYC on transcription during the DNA double-strand break response by RNA-seq of newly synthesized transcripts
(Submitter supplied) We sequenced newly synthesized mRNA to determine which genes are differentially transcribed during the DNA double-strand break (DSB) response. Moreover, as the transcription factor MYC is repressed in a p53-dependent manner during the DSB response, we determined the effect of this repression on transcription by maintaining MYC above its basal expression level. To control for differences in cell size, we spiked in S. 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/GSE101nnn/GSE101738/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395319
Series		Accession: GSE101738	ID: 200101738

2777. Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma
(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 SNP array; Non-coding RNA profiling by array
Platforms: GPL16791 GPL6801 GPL17904 286 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102094/
Series		Accession: GSE102094	ID: 200102094

2778. Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq]
(Submitter supplied) Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal portion of the fallopian tube.  Serous tubal intraepithelial carcinoma (STIC) lesions are the putative precursor to HGSC and identifiable in ~50% of advanced stage cases. To better understand the molecular etiology of HGSCs, we report a multi-center integrated genomic analysis of advanced stage tumors with and without STIC lesions and normal tissues. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 85 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102073/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA396544
Series		Accession: GSE102073	ID: 200102073

2779. RNA-sequencing profiles of five different pancreas cancer cell lines that were engineered to express a form of the basic helix-loop-helix transcription factor, E47, that localizes to the nucleus in response to tamoxifen.
(Submitter supplied) E47 had been shown previously to inhibit cell cycle progression in pancreas cancer cell lines. This study was designed to identify global changes in gene expression that occurred in response to E47 with the goal of identifying molecular mechanisms involved inE47-mediated inhibition of the cell cycle.
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/GSE100nnn/GSE100327/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391336
Series		Accession: GSE100327	ID: 200100327

2780. Synergistic activity and heterogeneous acquired resistance of combined MDM2 and MEK inhibition in KRAS mutant cancers
(Submitter supplied) There are currently no effective targeted therapies for KRAS mutant cancers. Therapeutic strategies that combine MEK inhibitors with agents that target apoptotic pathways may be a promising therapeutic approach. We investigated combining MEK and MDM2 inhibitors as a potential treatment strategy for KRAS mutant non-small cell lung cancers and colorectal carcinomas that harbor wild-type TP53. The combination of pimasertib (MEK inhibitor) + SAR405838 (MDM2 inhibitor) was synergistic and induced the expression of PUMA and BIM, led to apoptosis and growth inhibition in vitro, and tumor regression in vivo. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 198 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99015/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387004
Series		Accession: GSE99015	ID: 200099015

2781. Identification of splice variants and RNA binding partners of STAT3-induced long noncoding RNAs (STAiRs) in multiple myeloma
(Submitter supplied) Interleukin 6 (IL-6) activates the transcription factor signal transducer and activator of transcription 3 (STAT3). We previously identified several STAT3-induced long noncoding RNAs (STAiRs) in INA-6 multiple myeloma cells (Hackermüller et al. 2014). Here, we analyze five STAiRs by CAPTURE- and ChIRP-RNA-sequencing, a pulldown of a target RNA by transcript tiling oligonucleotides. The CAPTURE technique allows the identification of different STAiR splice variants and shall give rise to the transcript architecture. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL15520 14 Samples
FTP download: GEO (TAR) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95131/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376176
Series		Accession: GSE95131	ID: 200095131

2782. Enhancer reprogramming promotes pancreatic cancer progression and metastasis
(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: GPL18573 GPL19057 136 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99311/
Series		Accession: GSE99311	ID: 200099311

2783. Enhancer reprogramming promotes pancreatic cancer progression and metastasis [RNA-seq]
(Submitter supplied) Pancreatic ductal adenocarcinoma (PDA) is one of the most lethal human malignancies, owing in part to its propensity for metastasis. Here, we used an organoid culture system to investigate how transcription and the enhancer landscape become altered during each stage of PDA progression. This approach revealed that the metastatic transition is accompanied by massive, and recurrent alterations in enhancer activity. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL19057 GPL18573 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388127
Series		Accession: GSE99310	ID: 200099310

2784. Cytokine Stimulation of PTPN2-deleted cancer cells
(Submitter supplied) PTPN2 was deleted from a selection of murine and human cancer cells using CRISPR/Cas9. The loss-of-function phenotype was assessed in vitro with cytokine stimulation or vehicle control.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL21697 GPL21626 81 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388068
Series		Accession: GSE99299	ID: 200099299

2785. LMO1 Synergizes with MYCN to Promotes Neuroblastoma Initiation and Metastasis 
(Submitter supplied) High levels of LMO1 expression synergizes with MYCN to accelerate neuroblastomagenesis, enhance disease penetrance and promote widespread metastasis in zebrafish. Transcriptomic analysis of human neuroblasotma cells with programed expression of LMO1 vs vector control or neuroblastoma cells with differential endogenous LMO1 expression revealed that gene signitures affecting tumor cell-extracellular matrix interaction are significantly associated with high levels of LMO1 expression. 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/GSE90nnn/GSE90087/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354383
Series		Accession: GSE90087	ID: 200090087

2786. Epigenetic silencing of the tumor suppressor RASSF4 favors multiple myeloma progression
(Submitter supplied) RAS is frequently mutated in multiple myeloma (MM) leading to aberrant signaling. Next to their classical oncogenic effects, RAS proteins also mediate anti-tumor effects through the Ras-Association Domain Family (RASSF) proteins. Currently, no data about the role of RASSF proteins in MM disease is available. Here we report that RASSF4 is downregulated during MM progression, correlating with a bad prognosis. 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/GSE85nnn/GSE85020/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335945
Series		Accession: GSE85020	ID: 200085020

2787. Gene regulation of candidate cancer gene DIP2C
(Submitter supplied) Purpose: The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in breast and lung cancers. We want to understand the role of DIP2C in tumor development. Methods: We engineered human DIP2C knockout cell systems by genome editing, and then use next-generation sequencing to identify the genes affected by the loss of DIP2C. Results: Inactivation of DIP2C triggers substantial gene expression changes, cellular senescence and epithelial to mesenchymal transition in cancer cells.
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/GSE80nnn/GSE80746/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA319905
Series		Accession: GSE80746	ID: 200080746

2788. RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment
(Submitter supplied) To elucidate whether F. nucleatum plays a role in colorectal cancer tumorigenesis,  RNA-seq analysis was performed to compare the gene expression profiles of F. nucleatum treated HT-29 cell line or not.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL21290 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90944/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356417
Series		Accession: GSE90944	ID: 200090944

2789. Neural Precursor Cell-Derived Pleiotrophin Mediates Glioma Invasion of the Subventricular Zone
(Submitter supplied) The lateral ventricle subventricular zone (SVZ) is a frequent and consequential site of pediatric and adult glioma spread, but the cellular and molecular mechanisms mediating this are poorly understood. We demonstrate that neural precursor cell (NPC):glioma cell communication underpins this propensity of glioma to colonize the SVZ through secretion of chemoattractant signals toward which glioma cells home. 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/GSE99nnn/GSE99812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389704
Series		Accession: GSE99812	ID: 200099812

2790. The role of FAM46C in myeloma cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Expression profiling by array
Platforms: GPL11154 GPL17586 11 Samples
FTP download: GEO (CEL, CHP) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99358/
Series		Accession: GSE99358	ID: 200099358

2791. The role of FAM46C in myeloma cells [sequencing]
(Submitter supplied) FAM46C is one of the most recurrently mutated genes in multiple myeloma (MM), however its role in disease pathogenesis is not determined. Here we demonstrate that wild type (WT) FAM46C overexpression induces substantial cytotoxicity in MM cells. In contrast, FAM46C mutations found in MM patients abrogate this cytotoxicity indicating a MM survival advantage conferred by the FAM46C mutant phenotype. WT FAM46C overexpression downregulated IRF4, CEBPB, MYC and upregulated immunoglobulin (Ig) light chain and HSPA5/BIP. 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/GSE99nnn/GSE99356/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388199
Series		Accession: GSE99356	ID: 200099356

2792. CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair
(Submitter supplied) BACKGROUND: Deletion of the chromatin remodeler CHD1 is a common genomic alteration found in human prostate cancers (PCas). CHD1 loss represents a distinct PCa subtype characterized by SPOP mutation and higher genomic instability [1-3]. However, the role of CHD1 in PCa development in vivo and its clinical utility remain unclear. DESIGN: To study the role of CHD1 in PCa development and its loss in clinical management, we generated a genetically engineered mouse model with prostate-specific deletion of murine Chd1 as well as isogenic CHD1 WT and homozygous deleted human benign and PCa lines. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL11154 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84610/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330629
Series		Accession: GSE84610	ID: 200084610

2793. SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRD4_JQ1_RNA-seq)
(Submitter supplied) Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics of cancers including prostate cancer.  The E3 ubiquitin ligase adaptor protein speckle-type POZ protein (SPOP) is implicated in human prostate cancers due to its frequent mutation.  Here we demonstrate that SPOP binds to the BET proteins BRD2, BRD3 and BRD4.  Wild-type SPOP, but not prostate cancer-associated mutants, promotes polyubiquitination and proteasome degradation of BET proteins by recognizing a common degron motif. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78213/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA312942
Series		Accession: GSE78213	ID: 200078213

2794. BRCA1-mimetic compound NSC35446.HCl inhits IKKB expression by reducing estrogen receptor alpha occupancy in the IKKB promoter and inhibts NF-κB activity in anti-estrogen resitant human breast cells
(Submitter supplied) We previously identified small molecules that fit into a BRCA1-binding pocket within estrogen receptor-alpha (ER), mimic the ability of BRCA1 to inhibit ER activity (“BRCA1-mimetics”), and overcome antiestrogen resistance. One such compound, the hydrochloride salt of NSC35446 (“NSC35446.HCl”), also inhibited growth of antiestrogen-resistant LCC9 tumor xenografts. The purpose of this study was to investigate the down-stream effects of NSC35446.HCl and its mechanism of action. 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/GSE101691/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395214
Series		Accession: GSE101691	ID: 200101691

2795. PRDM1 inhibits proliferation of human colon cancer organoids
(Submitter supplied) We reports the transcript landscape of PR Domain Containing 1, with ZNF domain (PRDM1)  in RKO colon cancer cells. We show that PRDM1 alpha and PRDM1 beta transcript isoforms repress and activate a largely overlapping suite of genes, many of which belong to the embryonic stem cell core transcript program.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 12 Samples
FTP download: GEO (CSV, FPKM_TRACKING, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101668/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395153
Series		Accession: GSE101668	ID: 200101668

2796. SPOP mutation confers intrinsic BET inhibitor resistance in 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: GPL11154 26 Samples
FTP download: GEO (BIGWIG, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE88nnn/GSE88872/
Series		Accession: GSE88872	ID: 200088872

2797. Reprogramming of human stem cells towards a rejuvenated and transformation-resisting state by recoding a single nucleotide
(Submitter supplied) Premature senescence-associated functional decay and neoplastic transformation of transplanted human stem cells or their derivatives represent two major roadblocks for regenerative medicine. Cellular senescence acts as a major mechanism antagonizing neoplastic transformation, and stem cells evading senescence are prone to oncogenic transformation. So far it is unknown whether there is any genetic code, rewriting of which can simultaneously brake cellular senescence and oncogenic transformation programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 12 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84694/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA330850
Series		Accession: GSE84694	ID: 200084694

2798. O-glcnAc reprograms cellular energetics
(Submitter supplied) Dysfunctional mitochondria and generation of reactive oxygen species (ROS) promote chronic diseases, which have spurred interest in the molecular mechanisms underlying these conditions. Previously, we have demonstrated that disruption of post-translational modification of proteins with β-linked N-acetylglucosamine (O- glcnAcylation) via overexpression of the O-glcnAc–regulating enzymes O- glcnAc transferase (OGT) or O- glcnAcase (OGA) impairs mitochondrial function. 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/GSE101nnn/GSE101642/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395053
Series		Accession: GSE101642	ID: 200101642

2799. Global Regulation of Alternative RNA Splicing by the SR-Rich Protein RBM39 CLIP-seq
(Submitter supplied) RBM39 is extensively involved in alternative splicing of RNA and helps regulate transcript levels. RBM39 may modulate alternative splicing similarly to U2AF65 by either directly binding to RNA or recruiting other splicing factors, such as U2AF65.
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/GSE101nnn/GSE101631/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA395038
Series		Accession: GSE101631	ID: 200101631

2800. Integrative genomics identifies the molecular basis of resistance to Azacytidine therapy in Myelodysplastic Syndromes
(Submitter supplied) RNA-seq of bone marrow CD34+ cells of myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) patients to identify at the molecular pathways involved in primary resistance to AZA therapy.
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/GSE76nnn/GSE76203/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306622
Series		Accession: GSE76203	ID: 200076203

2801. The role of histone demethylase KDM5C in super-enhancer 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: GPL16791 12 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101565/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394840
Series		Accession: GSE101565	ID: 200101565

2802. Stapled peptide inhibitors of RAB25 target context-specific phenotypes in cancer
(Submitter supplied) The Ras-family small GTPase RAB25 is involved in numerous aspects of endosomal protein trafficking and cell polarity. Recent evidence has established a role for RAB25, as well as related RAB-family and effector proteins, in oncogenic signaling, highlighting the need for chemical probes targeting this class of proteins. Here we report the development of all-hydrocarbon stabilized peptides targeting RAB25 derived from the RAB-binding FIP-family of proteins. 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/GSE101528/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA394735
Series		Accession: GSE101528	ID: 200101528

2803. TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation
(Submitter supplied) EZH2 is generally associated with H3K27 methylation and gene silencing. Mass spectrometry of the EZH2-interactome in MCF7 cells revealed EZH2-interactions with SWI/SNF subunits and TRIM28, which formed a complex with EZH2 distinct from PRC2. Transcriptome profiling showed that EZH2 primarily activates transcription in MCF7 cells and with TRIM28 co-regulates a set of genes associated with stem cell maintenance and poor survival of breast cancer patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (WIG, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76271/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306771
Series		Accession: GSE76271	ID: 200076271

2804. Inhibitors of the histone methyltransferases EZH2/1 induce a potent antiviral state and suppress infection by diverse viral pathogens [RNA-Seq]
(Submitter supplied) Epigenetic regulation is based upon a network of complexes that modulate the chromatin character and structure of the genome to impact gene expression, cell fate, and development.  Thus, epigenetic modulators represent novel therapeutic targets to treat a range of diseases including malignancies.  Infectious pathogens such as herpesviruses are also regulated by cellular epigenetic machinery, and epigenetic therapeutics represent a novel approach to control infection, persistence, and the resulting recurrent disease. more...
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/GSE99nnn/GSE99839/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389770
Series		Accession: GSE99839	ID: 200099839

2805. Effects of plasticizers (bisphenol A, bisphenol AF) and an herbicide in MCF7 human breast cancer cells
(Submitter supplied) We studied alterations in gene expression profiles of the MCF7 human breast cancer cells caused by bisphenol A, bisphenol AF and glyphosate using Illumina RNA sequencing platform.
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/GSE87nnn/GSE87701/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345603
Series		Accession: GSE87701	ID: 200087701

2806. ARID1A-mutated ovarian cancers depend on HDAC6 activity
(Submitter supplied) ARID1A, encoding a subunit of the SWI/SNF chromatin remodeling complex, is the most mutated epigenetic regulator in human cancers.   ARID1A and TP53 mutations are typically mutually exclusive.  Therapeutic approaches that correlate with ARID1A mutational status remain a challenge. Here, we show that HDAC6 activity is essential in ARID1A-mutated ovarian cancers.  Inhibition of HDAC6 activity using a clinically applicable small molecule inhibitor significantly improved the survival of mice bearing ARID1A-mutated ovarian tumors. 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/GSE84nnn/GSE84405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329095
Series		Accession: GSE84405	ID: 200084405

2807. Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [RNA-seq]
(Submitter supplied) The success of targeted therapies hinges on our ability to understand the molecular and cellular mechanism of action of these agents. Here we modify various BET bromodomain inhibitors, an exemplar novel targeted therapy, to create functionally conserved compounds that are amenable to click-chemistry and can be used as molecular probes in vitro and in vivo. Using click-proteomics and click-sequencing we provide new mechanistic insights to explain the gene regulatory function of BRD4 and the transcriptional changes invoked by BET inhibitors. 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/GSE88nnn/GSE88750/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA348451
Series		Accession: GSE88750	ID: 200088750

2808. Identifying ASCL1 target genes in primary GBM stem cell cultures [RNA-seq]
(Submitter supplied) ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures. We sought to identify targets of ASCL1 in primary human GSC cultures. In this dataset, we include RNA-seq data obtained from GSC cultures harbouring a CRISPR-deletion of ASCL1. We assessed differential gene expression between control and GSC cultures induced to overexpress ASCL1 after 7 days of doxycycline treatment.
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/GSE87nnn/GSE87617/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345386
Series		Accession: GSE87617	ID: 200087617

2809. ASCL1 mediates neuronal differentiation of primary GBM stem cell cultures upon Notch signalling blockade [RNA-seq]
(Submitter supplied) ASCL1 mediates neuronal differentiation of GBM stem cell (GSC) cultures upon Notch signalling inhibition. We sought to identify gene expression changes that were specific to ASCL1 function. In this dataset, we include RNA-seq data obtained from GSC cultures harbouring wildtype or CRISPR-deletion of ASCL1. We assessed differential gene expression between wildtype and ASCL1-knockout after treatment with gamma-secretase inhibitor for 7 days.
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/GSE87nnn/GSE87615/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345387
Series		Accession: GSE87615	ID: 200087615

2810. SUMOylation Regulates miR-34b/c Targeted Gene Expression Program [RNA-seq]
(Submitter supplied) The microRNAs known as miR-34 family suppress the expression of a suit of proteins involved in oncogenesis and pluripotency, including c-Myc.  Their expression is frequently down regulated in cancers; however the regulation of their expression is not well understood. Through genome-wide miRNA profiling and mechanistic analysis, we identified an important role of SUMOylation in miR-34b/c expression, regulating the expression of c-Myc and all other tested miR-34 targets.
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/GSE101168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393835
Series		Accession: GSE101168	ID: 200101168

2811. Phenotype-driven precision oncology in patient-derived tumor models predict therapeutic response in squamous cell carcinoma
(Submitter supplied) Comparison of single-cell transcriptomic profiles of cell lines obtained from the primary and metastatic tumor from a single patient.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 152 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84323/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329106
Series		Accession: GSE84323	ID: 200084323

2812. RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation.
(Submitter supplied) The stepwise and sequential expression of viral genes underlies progression of the infectious life cycle. The Epstein-Barr virus (EBV) is both a tractable model for elucidating principles of transcription as well as a global health threat. We describe an experimental protocol and bioinformatics pipeline for functional identification of EBV true late genes, the last step of transcription prior to virion packaging and egress. more...
Organism:	Homo sapiens; Human gammaherpesvirus 4
Type:		Expression profiling by high throughput sequencing
Platform: GPL23185 12 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96689/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379377
Series		Accession: GSE96689	ID: 200096689

2813. RNAseq analysis of chemotherapy and radiation therapy-naïve breast tumors
(Submitter supplied) Assessment of chemo- and radiation therapy-naïve biopsy-confirmed invasive human breast tumors by RNAseq.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 103 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100925/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393443
Series		Accession: GSE100925	ID: 200100925

2814. Transcriptional Consequences of XPA Disruption in Human Cell Lines
(Submitter supplied) Purpose: Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100855/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393295
Series		Accession: GSE100855	ID: 200100855

2815. A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease
(Submitter supplied) This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue.  Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 134 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326727
Series		Accession: GSE83687	ID: 200083687

2816. Identification of downstream genes regulated by YAP1 through knockdown and overexpression of YAP1 in U251 cell with a stably expression of mutant APP
(Submitter supplied) Upstream regulator genes are central hub nodes in a network and their expression may response to  upstream trigger factors of a disease and influence expression of hundreds of downstream genes, and further facilitate disease development. Therefore, the identification of upstream regulator genes are vital for understanding the pathophysiology of the disease and seek for potential therapeutic targets for the treatment of the disease. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100891/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA393355
Series		Accession: GSE100891	ID: 200100891

2817. EWS-FLI1 represses Rho-actin signaling via MRTFB/YAP-1/TEAD perturbation in Ewing Sarcoma
(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: GPL570 GPL11154 58 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92741/
Series		Accession: GSE92741	ID: 200092741

2818. EWS-FLI1 represses Rho-actin signaling via MRTFB/YAP-1/TEAD perturbation in Ewing Sarcoma [RNA-Seq]
(Submitter supplied) Ewing Sarcoma (EwS) is a EWS-FLI1- fusion driven pediatric bone cancer with high metastatic potential. Cellular plasticity, typically regulated via the Rho-pathway, is a prerequisite for metastasis initiation. Here we interrogated the role of the Rho transcriptional effectors MRTFA/B in EwS. We find MRTFB transcriptional function strongly repressed by EWS-FLI1. Under EWS-FLI1-low (knock-down) conditions, MRTFB is activated and antagonizes global EWS-FLI1-dependent transcription. 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/GSE92nnn/GSE92739/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358639
Series		Accession: GSE92739	ID: 200092739

2819. Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures [RNA-Seq]
(Submitter supplied) DTP heterochromatin in genomic repeat regions protects the population from drug-induced death.
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/GSE100nnn/GSE100751/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392914
Series		Accession: GSE100751	ID: 200100751

2820. Repression of stress-induced LINE-1 expression protects cancer cell populations from lethal drug-exposures
(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: GPL18573 GPL16791 51 Samples
FTP download: GEO (BED, BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74180/
Series		Accession: GSE74180	ID: 200074180

2821. HTS-Seq analysis of Hela cells treated with NC ASO or snoRD50a ASOs
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL9115 14 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98221/
Series		Accession: GSE98221	ID: 200098221

2822. RNA-biotin based pull down assay with Hela Nuclear Extract followed by RNA-seq
(Submitter supplied) We aimed to discover trans-acting RNA molecules involved in mRNA 3’ processing. We reasoned that, if there exist such functional RNAs, they must directly associate with the key machinery responsible for mRNA 3’ processing. Therefore, it would be of great value to comprehensively identify RNAs interacting with pre-mRNA 3’ processing complex. To this goal, we took advantage of previously well-characterized system combined with high-throughput sequencing to investigate the target RNAs at the transcriptomic level. more...
Organism:	Homo sapiens
Type:		Other; Expression profiling by high throughput sequencing
Platform: GPL9115 2 Samples
FTP download: GEO (CSV, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98218/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384324
Series		Accession: GSE98218	ID: 200098218

2823. Glucose impairs tamoxifen sensitivity modulating CTGF in breast cancer cells
(Submitter supplied) Metabolic diseases, including type 2 diabetes and obesity are relevant negative prognostic factor in patients with breast cancer (BC). We have investigated the mechanisms through which elevated glucose levels affect tamoxifen sensitivity of estrogen receptor positive (ER+) BC cells. We found that MCF7 BC cell sensitivity to tamoxifen was 2-fold reduced in 25mM glucose (HG), a concentration mimicking hyperglycaemia, compared to 5.5 mM glucose (LG), resembling normal fasting glucose levels in humans. 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/GSE97nnn/GSE97647/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382560
Series		Accession: GSE97647	ID: 200097647

2824. Overexpression of NFIB and YBX1 in MCF-7 cells
(Submitter supplied) Studying transcription factor (TF) interactions and gene regulatory networks in breast cancer, we have recently identified two distinct and opposing clusters of TFs associated with estrogen receptor-positive and -negative breast cancer and breast cancer risk. The relative activity of these two groups of TFs has a dramatic effect on patient outcomes and is likely to influence the phenotypic plasticity observed in breast cancer. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95299/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376585
Series		Accession: GSE95299	ID: 200095299

2825. GCTM-5 positive and negative cells in pancreatic adenocarcinoma cell lines
(Submitter supplied) Analysis of GCTM-5 positive and negative cells sorted from CFPAC-1 and SW1990 human pancreatic adenocarcinoma cell line. Results provide insight into molecular characteristics of GCTM-5 positive 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/GSE95nnn/GSE95176/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376281
Series		Accession: GSE95176	ID: 200095176

2826. Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL15520 GPL16791 GPL18573 23 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93078/
Series		Accession: GSE93078	ID: 200093078

2827. Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [ppp5end RNA-Seq]
(Submitter supplied) The goal of this study is to investigate if endogenous RNA in exosomes activates RIG-I through unshielding.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93073/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359793
Series		Accession: GSE93073	ID: 200093073

2828. Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [patients RNA-Seq]
(Submitter supplied) The goal of this study is to investigate if endogenous RNA in exosomes activates RIG-I through unshielding.
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/GSE93nnn/GSE93072/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359792
Series		Accession: GSE93072	ID: 200093072

2829. Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [RNA-Seq]
(Submitter supplied) The goal of this study is to investigate if endogenous RNA in exosomes activates RIG-I through unshielding.
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/GSE93nnn/GSE93071/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359786
Series		Accession: GSE93071	ID: 200093071

2830. Virus Mimicry in the Tumor Microenvironment Activates RIG-I Through Unshielding of Endogenous RNA in Exosomes [exoRNA-Seq]
(Submitter supplied) The goal of this study is to investigate if endogenous RNA in exosomes activates RIG-I through unshielding.
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/GSE93nnn/GSE93070/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA359787
Series		Accession: GSE93070	ID: 200093070

2831. Heterogeneity of neuroblastoma cell identity revealed by transcriptional circuitries
(Submitter supplied) Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neural crest cells (NCCs). To define Core Regulatory Circuitries (CRCs) controlling the gene expression program of neuroblastoma, we established and analyzed the neuroblastoma super-enhancer landscape. We discovered three types of identity in neuroblastoma cell lines: a sympathetic noradrenergic identity defined by a CRC module including the PHOX2B, HAND2 and GATA3 transcription factors (TFs); an NCC-like identity, driven by a CRC module containing AP-1 family TFs; a mixed type further deconvoluted at the single cell level. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL16791 101 Samples
FTP download: GEO (BED, BW, NARROWPEAK, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90683/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355381
Series		Accession: GSE90683	ID: 200090683

2832. Transcriptomic analysis of an archived bladder cancer cohort
(Submitter supplied) Establishment and application of RNAseq based transcriptome analayis on an archivaed bladder cancer cohort.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL15520 67 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59483/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA255416
Series		Accession: GSE59483	ID: 200059483

2833. Immunophenotyping and Transcriptomic Outcomes in PDX-Derived TNBC Tissue
(Submitter supplied) Cancer tissue functions as an ecosystem of a diverse set of cells that interact in a complex tumor microenvironment. Genomic tools applied to biopsies in bulk fail to account for this tumor heterogeneity, whereas single-cell imaging methods limit the number of cells which can be assessed or are very resource intensive. The current study presents methods based on flow cytometric analysis and cell sorting using known cell surface markers (CXCR4/CD184, CD24, THY1/CD90) to identify and interrogate distinct groups of cells in triple-negative breast cancer clinical biopsy specimens from patient-derived xenograft (PDX) models. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (TXT, XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100669/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392464
Series		Accession: GSE100669	ID: 200100669

2834. BET inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Human gammaherpesvirus 4
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms: GPL22131 GPL23362 GPL22132 106 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84214/
Series		Accession: GSE84214	ID: 200084214

2835. BET inhibitors suppress lytic DNA replication [Akata-Zta RNA-seq]
(Submitter supplied) Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. more...
Organism:	Human gammaherpesvirus 4; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL22132 18 Samples
FTP download: GEO (WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84211/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328406
Series		Accession: GSE84211	ID: 200084211

2836. BET inhibitors suppress BZLF1 expression [MutuI RNA-seq]
(Submitter supplied) Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. more...
Organism:	Human gammaherpesvirus 4; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL22131 12 Samples
FTP download: GEO (WIG, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA328391
Series		Accession: GSE84209	ID: 200084209

2837. The FAM46C gene encodes a non-canonical poly(A) polymerase and acts as an onco-suppressor in multiple myeloma
(Submitter supplied) FAM46C is one of the most frequently mutated genes in multiple myeloma (MM) and encodes a protein of unknown function. Using a combination of in vitro and in vivo approaches, we demonstrate that FAM46C encodes an active cytoplasmic non-canonical poly(A) polymerase, which enhances mRNA stability and gene expression. Moreover, we also found that the reintroduction of active FAM46C into MM cell lines, but not its catalytically-inactive mutant, leads to broad polyadenylation and stabilization of mRNAs strongly enriched with those encoding endoplasmic reticulum-targeted proteins and induced cell death. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 26 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83772/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326952
Series		Accession: GSE83772	ID: 200083772

2838. Gene profiling of human adult and pediatric liver cancer cells
(Submitter supplied) In an effort to comprehend some of the molecular differences between two cancers that originate in the same tissue, adult HCC and pediatric HB, we profiled four HCC and four HB cell lines using RNA sequencing. We identified an enhanced sugar uptake and usage in HB tumors compared to adult HCC, and two different metabolic subtypes of HB. We identified an enhanced sugar uptake and usage in HB tumors compared to adult HCC, and two different metabolic subtypes of HB. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 16 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326261
Series		Accession: GSE83518	ID: 200083518

2839. Convergent roles of ATF3 and CSL in chromatin control of CAF activation
(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: GPL11154 GPL16791 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81406/
Series		Accession: GSE81406	ID: 200081406

2840. Convergent roles of ATF3 and CSL in chromatin control of CAF activation [RNA-seq]
(Submitter supplied) Cancer associated fibroblasts (CAFs) play an important role in initiating and promoting epithelial cancers. The specific chromatin modifications involved in CAF activation remain to be elucidated. CSL, a constitutive transcriptional repressor and mediator of canonical Notch signaling, functions as a direct negative regulator of CAF effector genes and suppresses cancer/stromal cell expansion. We find that ATF3, a key stress responsive transcriptional repressor up-regulated in the acute UVA response of skin fibroblasts, is down-modulated in stromal cells of premalignant skin SCC lesions similarly to CSL. more...
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/GSE81nnn/GSE81405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321476
Series		Accession: GSE81405	ID: 200081405

2841. IFNγ-dependent tissue immune homeostasis is co-opted in the tumor microenvironment
(Submitter supplied) Homeostatic programs maintain equilibrium between immune protection, and selftolerance. Such mechanisms impact autoimmunity and tumor formation, respectively. How tissue homeostasis is maintained, and impacts tumor surveillance is unknown. Here we identify that mononuclear phagocytes share conserved programming during homeostatic differentiation, and entry into tissue. IFNγ is necessary and sufficient to induce these transcripts, revealing a key instructive role. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 333 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100337/
Series		Accession: GSE100337	ID: 200100337

2842. LTR-retrotransposon control by tRNA-derived small RNA
(Submitter supplied) Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, LTR-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 Lysine 9 trimethylation in preimplantation stem cells. We found abundant, 18 nt tRNA-derived small RNA (tRF) in these cells, and ubiquitously expressed 22 nt tRFs, that include the 3' terminal CCA of mature tRNAs, and target the tRNA primer binding site (PBS) essential for ERV reverse transcription. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
4 related Platforms 54 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82199/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324286
Series		Accession: GSE82199	ID: 200082199

2843. RNA sequencing of T-ALL (COG study)
(Submitter supplied) The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure or relapse.  We investigated 213 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Studies 9404 and 0434 and identified a cluster cases characterized by increased expression of HOX9/10.  In samples with >8-fold HOXA9/10 deregulation, the presence of specific molecular lesions were confirmed through a systematic review of cytogenetic databases, FISH and PCR testing. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL17303 17 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71359/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291023
Series		Accession: GSE71359	ID: 200071359

2844. Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression [RNA-Seq]
(Submitter supplied) Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regression to life-threatening progression. High-risk neuroblastoma patients receive myeloablative chemotherapy with hematopoietic stem-cell transplant followed by adjuvant retinoid differentiation treatment. However, the overall survival remains low; hence, there is an urgent need for alternative therapeutic approaches. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 68 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100568/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA392124
Series		Accession: GSE100568	ID: 200100568

2845. Immune escape in breast cancer during in situ to invasive carcinoma transition
(Submitter supplied) To dissect mechanisms of immune escape during breast tumor progression, we analyzed the composition of leukocytes in normal breast tissues, ductal carcinomas in situ (DCIS), and HER2+ and triple negative invasive ductal carcinomas (IDC). We found significant tissue and tumor subtype-specific differences in multiple cell types including T cells and neutrophils. Analysis of gene expression profiles of T cells demonstrated enrichment for activated GZMB+MKI67+CD8+ effector T cell signatures in DCIS. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL16791 41 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87517/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA345006
Series		Accession: GSE87517	ID: 200087517

2846. Transcriptome profiles of moderate dysplasia in oral mucosa associated with malignant conversion
(Submitter supplied) Oral malignancies are among the top most deadly cancers in the world. Early diagnosis of oral premalignant and malignant lesions is essential for treatment decision-making and prognosis improvement. In this study, we systematically evaluated the gene expression patterns during the pathogenesis of oral moderate dysplasia. RNA sequencing detected 21556 genes in moderate dysplasia and paired normal tissues from three patients. 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/GSE72nnn/GSE72627/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA294509
Series		Accession: GSE72627	ID: 200072627

2847. Hypoxia is a Key Driver of Alternative Splicing in Human Breast Cancer Cells
(Submitter supplied) Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 3 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97317/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381392
Series		Accession: GSE97317	ID: 200097317

2848. Novel SF3B1 Deletion Mutations Result in Aberrant RNA Splicing in CLL Patients
(Submitter supplied) Recurrent mutations in RNA splicing factors SF3B1, U2AF1, and SRSF2 have been reported in hematologic cancers including myelodysplastic syndromes (MDS) and chronic lymphocytic leukemia (CLL). However, SF3B1 is the only splicing associated gene to be found mutated in CLL and has been shown to induce aberrant splicing. To investigate if any other genomic aberration caused similar transcriptome changes, we clustered RNASeq samples based on an alternative 3’ splice site (ss) pattern previously identified in SF3B1-mutant CLL patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95352/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA376727
Series		Accession: GSE95352	ID: 200095352

2849. Effect of MDK expressing Melanoma cells conditioned media in Human LEC
(Submitter supplied) Gene expression analysis in hLECs treated with gain of function or loss of function of MDK in human melanoma cells.
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/GSE94nnn/GSE94549/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371460
Series		Accession: GSE94549	ID: 200094549

2850. Zoledronic acid inhibits NFAT and IL-2 signaling pathways in regulatory T cells and diminishes their suppressive function in patients with metastatic cancer
(Submitter supplied) In order to identify the processes altered in T regulatory cells (Treg) by Zoledronic acid (ZA), we examined RNA expression by RNA-seq in Treg treated with and without ZA. We identified gene expression alterations in ZA-treated Treg that were essential to Treg function.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO (TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96075/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378764
Series		Accession: GSE96075	ID: 200096075

2851. RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction
(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 36 Samples
FTP download: GEO (BW, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87286/
Series		Accession: GSE87286	ID: 200087286

2852. RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction (RNA-Seq)
(Submitter supplied) RUNX1 is a frequent target of translocations in acute myeloid leukemia whereby its DNA binding domain fuses to different epigenetic regulators. To assess how different RUNX1 fusion proteins interact with the epigenome we compared the global binding patterns and the chromatin landscape of t(8;21) and t(3;21) AML which express RUNX1-ETO and RUNX1-EVI-1, respectively. We found that differential prognosis for these types of AML is reflected in fundamental differences in gene expression, chromatin landscape, binding patterns of the fusion proteins and other transcription factors as identified by genome-wide digital footprinting in patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 20 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87285/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343968
Series		Accession: GSE87285	ID: 200087285

2853. PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naïve ESCs
(Submitter supplied) Polycomb repressive complex 2 and the epigenetic mark that it deposits, H3K27me3, are evolutionarily conserved and play critical roles in development and cancer. However, their roles in cell fate decisions in early embryonic development remain poorly understood. Here we report that knockout of polycomb repressive complex 2 genes in human embryonic stem cells causes pluripotency loss and spontaneous differentiation toward a meso-endoderm fate, owing to de-repression of BMP signalling. 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/GSE92nnn/GSE92625/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358193
Series		Accession: GSE92625	ID: 200092625

2854. CUREfast: Accelerating research with families
(Submitter supplied) RNA sequencing of tissue samples taken from pediatric cancer patients of varying disease type. Patients represented those with terminal disease with samples taken from resection or autopsy.
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/GSE100nnn/GSE100427/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391716
Series		Accession: GSE100427	ID: 200100427

2855. Altered gene expression by C1orf106 in papillary thyroid cancer cells
(Submitter supplied) Chromosome 1 open reading frame 106 (C1orf106) has been shown to be elevated in lung adenocarcinoma. However, its expression and function in papillary thyroid cancer (PTC) are totally unknown. To explore the role of C1orf106 in PTC, we analyzed the gene expression in TPC1 cells with or without C1orf106 overexpression.
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/GSE100nnn/GSE100392/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391505
Series		Accession: GSE100392	ID: 200100392

2856. Gene expression and 4sUDRB-seq for NF90/NF110 of human scramble and KD HeLa cells.
(Submitter supplied) We have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human HeLa cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 18 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90874/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356263
Series		Accession: GSE90874	ID: 200090874

2857. Expression profiling of lncRNAs, miRNAs and mRNAs and their differential expression in leiomyoma using next generation RNA sequencing
(Submitter supplied) Total RNA was isolated from leiomyoma and paired myometrium (N=8) and samples from three pairs were subjected to RNA sequencing. After analysis, 5941 lncRNAs (2813 up- and 3128 down-regulated at ≥1.5 fold), 148 miRNAs (56 up- and 96 down-regulated at ≥1.5 fold) and 3855 mRNAs (2030 up- and 1855 down-regulated at ≥1.5 fold) were differentially expressed in leiomyomas. Using QRT-PCR we further confirmed the expression of HULC, lnc-MEG3, LINC00890, TSIX, LINC00473, lnc-KLF9-1 and lnc-POTEM-3 (lncRNA-ATB) in leiomyoma and matched myometrium (N=8). 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/GSE100nnn/GSE100338/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391373
Series		Accession: GSE100338	ID: 200100338

2858. Field cancerized fibroblasts in primary culture, P2
(Submitter supplied) Fibroblasts cultured from human breast cancer and adjacent normal tissues at 1cm and 5cm from the margin.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 9 Samples
FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83611/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326500
Series		Accession: GSE83611	ID: 200083611

2859. Assessing the developmental and malignant potential of human pluripotent stem cells by RNA-seq analysis of Teratomas
(Submitter supplied) The International Stem Cell Initiative compared three common approaches for assessing pluripotent stem cells (PSC).  The formation of teratomas in vivo, or embryoid bodies (EB) in vitro, provide direct tests of differentiation, whereas PluriTest predicts pluripotency through bioinformatic analysis of transcriptomes of undifferentiated cells.  We studied the teratomas by histology and TeratoScore, which analyzes gene expression in each tumor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 37 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100223/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA391086
Series		Accession: GSE100223	ID: 200100223

2860. Assessing the developmental and malignant potential of human pluripotent stem 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
Platforms: GPL11154 GPL10558 GPL23322 644 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97964/
Series		Accession: GSE97964	ID: 200097964

2861. TCF7L1 knockdown in pancreatic cancer
(Submitter supplied) RNAi mediated depletion of TCF7L1 increases activity of a Wnt-based reporter and imparts more aggressive tumor phenotypes in vitro in pancreatic cancer cell lines that express TCF7L1. We sought to determine what changes in transcription ocurred after RNAi mediated knockdown of TCF7L1 in these cells by RNA-sequencing
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/GSE90nnn/GSE90926/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356377
Series		Accession: GSE90926	ID: 200090926

2862. Aneuploidy triggers an immune response
(Submitter supplied) Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways exist that limit the prevalence of such cells? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells. 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/GSE83nnn/GSE83647/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326596
Series		Accession: GSE83647	ID: 200083647

2863. AML1-ETO induces leukemia via C/D box snoRNA/RNPs.
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by array; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing
4 related Platforms 94 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80602/
Series		Accession: GSE80602	ID: 200080602

2864. Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 109 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90730/
Series		Accession: GSE90730	ID: 200090730

2865. Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [HNSCC]
(Submitter supplied) Therapies that boost the anti-tumor responses of cytotoxic lymphocytes (CTLs) have shown promise in the clinic. However, clinical responses to currently available immunotherapeutic agents vary considerably, for which the molecular basis is unclear. To date, unbiased transcriptomic studies of CTLs in human cancers have been performed in whole tumors or cells obtained from peripheral blood or metastatic sites of heavily pre-treated patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 41 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90729/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355637
Series		Accession: GSE90729	ID: 200090729

2866. Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [NSCLC]
(Submitter supplied) Therapies that boost the anti-tumor responses of cytotoxic lymphocytes (CTLs) have shown promise in the clinic. However, clinical responses to currently available immunotherapeutic agents vary considerably, for which the molecular basis is unclear. To date, unbiased transcriptomic studies of CTLs in human cancers have been performed in whole tumors or cells obtained from peripheral blood or metastatic sites of heavily pre-treated patients. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 68 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90728/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355638
Series		Accession: GSE90728	ID: 200090728

2867. Colonic Organoids Derived from Human Pluripotent Stem Cells for Modeling Colorectal Cancer and Drug Discovery
(Submitter supplied) mRNA expression from tubular adenomas of patients with Familial Adenomatous Polyposis
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/GSE88945/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA349164
Series		Accession: GSE88945	ID: 200088945

2868. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases
(Submitter supplied) Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3’ end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here we show that the nuclear canonical (PAPalpha and PAPgamma) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 7 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84461/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA329255
Series		Accession: GSE84461	ID: 200084461

2869. Total RNA sequencing of APC mutant and wt colonic organoids
(Submitter supplied) We report elevated expression levels of genes involved in colon cancer in samples that carry mutations in the APC gene. Mutated skin fibroblasts were reprogrammed to iPSCs and then differentiated to colonigc organoids, where the total RNA was extracted from.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL20301 8 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77250/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA309855
Series		Accession: GSE77250	ID: 200077250

2870. Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast 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 high throughput sequencing
Platforms: GPL9442 GPL10999 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74943/
Series		Accession: GSE74943	ID: 200074943

2871. Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast cancer [RNA-seq]
(Submitter supplied) Approximately 75% of breast cancers express estrogen receptor α (ERα) and depend on estrogen signals for continued growth. Aromatase inhibitors (AIs) prevent estrogen production and inhibit estrogen receptor signaling, resulting in decreased cancer recurrence and mortality. Advanced tumors treated with AIs almost always develop resistance to these drugs via the up-regulation of alternative growth signals. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 2 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74941/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA301976
Series		Accession: GSE74941	ID: 200074941

2872. RNA-sequencing in MDA-231-D cells transfected with ZEB1 or ZEB2 siRNAs
(Submitter supplied) We searched for roles of ZEB1and/or ZEB2 during EMT by RNA-seq in breast cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 5 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384523
Series		Accession: GSE98273	ID: 200098273

2873. ZEB1-regulated inflammatory phenotype in breast cancer cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Zinc finger E-box binding protein 1 (ZEB1) and ZEB2 induce epithelial-mesenchymal transition (EMT) and cancer progression. However, little is known about global picture of transcriptional regulation by ZEB1 and ZEB2. Here we identified an inflammatory phenotype regulated by ZEB1 using chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) in basal type breast cancer cells, followed by gene set enrichment analysis (GSEA) of ZEB1-bound genes.
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL17303 12 Samples
FTP download: GEO (BED, BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89206/
Series		Accession: GSE89206	ID: 200089206

2874. RNA-sequencing in TGF-beta treated MDA-231-D cells transfected with ZEB1/ZEB2 siRNAs [RNA-seq]
(Submitter supplied) We searched for roles of ZEB1 during EMT by RNA-seq in breast cancer cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL17303 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89205/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA350680
Series		Accession: GSE89205	ID: 200089205

2875. RNA_seq and Ribo_seq analyses applied to PC9 and H1933 human cancer cell lines
(Submitter supplied) We used RNA-seq and Ribo-seq analyses to examine translation efficiency (TE) in PC9 and H1933 cells
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL9115 4 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96716/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379447
Series		Accession: GSE96716	ID: 200096716

2876. Next Generation Sequencing of Gene expression changes in U2OS osteosarcoma cells with PML silencing
(Submitter supplied) We used next generation sequencing to analyze the gene expression changes in U2OS osteosarcoma cells expressing shRNA targeting the promyelocytic leukemia (PML) gene transcripts
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15456 2 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94126/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369001
Series		Accession: GSE94126	ID: 200094126

2877. The RNA-seq (miRNA and mRNA) analysis of three human osteosarcoma cells
(Submitter supplied) RNA-seq analysis was performed by BGI-Tech of China, and RNA-seq library preparation and sequencing were performed by BGI (Shenzhen, China).
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL11154 4 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89930/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354296
Series		Accession: GSE89930	ID: 200089930

2878.  Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization
(Submitter supplied) Solid tumors are less oxygenated than normal tissues, and for this reason the cancer cells have developed several molecular mechanisms of adaptation to hypoxic environment. Moreover, his poor oxygenation is a major indicator of an adverse prognosis and leads resistance to standard anticancer treatment. Previous reports from this laboratory showed an involvement of Che-1/AATF (Che-1) in cancer cell survival under stress conditions, and on the basis of these observations, we hypothesized that Che-1 might have a role in the response of cancer cells to hypoxia. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 4 Samples
FTP download: GEO (BIGWIG, TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90599/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356445
Series		Accession: GSE90599	ID: 200090599

2879. PNET animal model: new insights
(Submitter supplied) Recently, we described a new animal model of CNS primitive neuroectodermal tumors (CNS-PNET), which was generated by orthotopic transplantation of human Radial Glial (RG) cells into NOD-SCID mice’s brain sub- ventricular zone. In the current study we conducted comprehensive RNA-Seq analyses to gain some insights on the mechanisms underlying tumorigenesis in this mouse model of CNS-PNET. Here we show that the RNA-Seq profiles derived from these tumors cluster with those reported for patients’ PNETs.
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/GSE82nnn/GSE82102/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324012
Series		Accession: GSE82102	ID: 200082102

2880. Characterizing isomer variants in the microRNA-34/449 family
(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: GPL20148 19 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77252/
Series		Accession: GSE77252	ID: 200077252

2881. Trascriptome of thyroid cancer-induced macrophages
(Submitter supplied) RNA sequencing data of macrophages after differentiation in the presence of TPC1 thyroid cancer cell line
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 16 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76445/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307316
Series		Accession: GSE76445	ID: 200076445

2882. Globally construct ceRNA regulation network based on comparison with SHEE and SHEEC cell lines (RNA-Seq)
(Submitter supplied) Long non-coding RNAs (lncRNAs), new star ncRNA class of mRNA-like transcripts, play complicate and critical roles in regulating various key biological processes including chromatin modification, transcription and post-transcriptional processing. Remarkably, some lncRNAs serve as a miRNA “sponge” to inhibit mediation of the differentiation of miRNA target in post-transcriptional regulation. Here, we firstly constructed the putative ceRNA network by integrating lncRNAs, miRNAs and mRNAs expression in compared with SHEE and SHEEC cell lines based on the high-though RNA sequencing data and microarray data. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL16791 2 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE72nnn/GSE72273/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA293566
Series		Accession: GSE72273	ID: 200072273

2883. Genomic Regulation of Invasion by STAT3 in Triple Negative Breast Cancer
(Submitter supplied) Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform: GPL11154 54 Samples
FTP download: GEO (BEDGRAPH, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85579/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA338851
Series		Accession: GSE85579	ID: 200085579

2884. Lipid catabolism inhibition sensitizes prostate cancer cells to antiandrogen blockade
(Submitter supplied) Prostate cancer (PCa) is the most common malignancy among western men and the second leading-cause of cancer related deaths. For men who develop metastatic, castration-resistant PCa (mCRPC), survival is limited, making the identification of novel therapies for mCRPC critical. Deficient lipid oxidation via carnitine palmitoyltransferase (CPT1) results in decreased growth and invasion, underscoring the role of lipid catabolism to fuel PCa growth. 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/GSE83nnn/GSE83547/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326312
Series		Accession: GSE83547	ID: 200083547

2885. hnRNP Q1 targeting RNA in colorectal cancer cell line SW480
(Submitter supplied) In order to study the potential targeting RNA of hnRNP Q1 in colorectal cancer, RNA immunoprecipitation were used for collecting hnRNP Q1-associated RNA.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10999 1 Sample
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76457/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA307345
Series		Accession: GSE76457	ID: 200076457

2886. Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood
(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 136 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99836/
Series		Accession: GSE99836	ID: 200099836

2887. Transcriptional profile of human iPSC and HIOs with APC mutations
(Submitter supplied) Background and Aims: mutations in the gene Adenomatous Polyposis Coli or APC appear in most sporadic cases of colorectal cancer and it is the most frequent mutation causing hereditary Familial Adenomatous Polyposis. The detailed molecular mechanism by which APC mutations predispose to the development of colorectal cancer is not completely understood. This is in part due to the lack of accessibility to appropriate models that recapitulate the early events associated with APC mediated intestinal transformation. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 48 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99821/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389724
Series		Accession: GSE99821	ID: 200099821

2888. Genome-scale Activation Screen Identifies a LncRNA Locus Regulating a Gene Neighborhood [RNA-Seq]
(Submitter supplied) The mammalian genome contains thousands of loci that transcribe long noncoding RNAs (lncRNAs), some of which are known to play critical roles in diverse cellular processes through a variety of mechanisms. While some lncRNA loci encode RNAs that act non-locally (in trans), emerging evidence indicates that many lncRNA loci act locally (in cis) to regulate expression of nearby genes—for example, through functions of the lncRNA promoter, transcription, or transcript itself. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 133 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99819/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA389719
Series		Accession: GSE99819	ID: 200099819

2889. Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of BET inhibitor JQ1
(Submitter supplied) We analyzed anti-proliferative dominant-negative Brd4 mutants that compete with the function of distinct Brd4 domains. We used these Brd4 mutants to compare the Brd4-specific transcriptome with the transcriptome of JQ1 treated cells.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 20 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92456/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA357609
Series		Accession: GSE92456	ID: 200092456

2890. Menin Enhances c-Myc-mediated Transcriptional Activity To Promote Cancer Progression
(Submitter supplied) MYC is a master regulator of transcription in growing cells. Menin is an enigmatic protein that displays unique ability to either suppress or promote tumorigenesis in a context dependent manner. It's interesting to ask is there any relationship between MYC and menin.Here, we used RNA-seq to study global transcriptomic expression of MYC or MEN1 knockdown HT1080 cells to investigate whether there are any correlations between MYC- and menin- regulated gene expression. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 9 Samples
FTP download: GEO (BED, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE86nnn/GSE86504/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA342098
Series		Accession: GSE86504	ID: 200086504

2891. Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours
(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: GPL17585 GPL11154 36 Samples
FTP download: GEO (CEL) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84788/
Series		Accession: GSE84788	ID: 200084788

2892. Compared performance of Affymetrix HTA arrays and Illumina RNAseq for the analysis of tumours [RNA-seq]
(Submitter supplied) Here we compared the performance of Affymetrix HTA 2.0 microarray and Illumina 2000 RNA-sequencing techniques on the clinical samples collected from patients with lung squamous cell carcinoma.
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/GSE84nnn/GSE84776/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA331133
Series		Accession: GSE84776	ID: 200084776

2893. Gene expression profiling of papillary thyroid cancer from central and invasive regions
(Submitter supplied) We analyzed the gene expression profile of papillary thyroid cancer from central and invasive regions.
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/GSE83nnn/GSE83560/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326345
Series		Accession: GSE83560	ID: 200083560

2894. Genome and transcriptome profiling of fibrolamellar carcinoma [RNA-Seq]
(Submitter supplied) Fibrolamellar hepatocellular carcinoma (FL-HCC) is a rare variant of HCC that most frequently affects young adults. Because of its rarity and an absence of preclinical models, the molecular biology of FL-HCC remains unclear. Our objective was to analyze chromosomal alterations and dysregulated gene expression in tumor specimens collected at a single center during two decades of experience with FL-HCC.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 35 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63018/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA266512
Series		Accession: GSE63018	ID: 200063018

2895. Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [VCaP RNA-Seq]
(Submitter supplied) Half of prostate cancers are caused by a gene-fusion that enables androgens to drive expression of the normally silent ETS transcription factor ERG in luminal prostate cells1-4.  Recent prostate cancer genomic landscape studies5-10 have reported rare but recurrent point mutations in the ETS repressor ERF11.  Here we show these ERF mutations cause decreased protein stability and ERF mutant tumours are mostly exclusive from those with ERG fusions. 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/GSE83nnn/GSE83652/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326603
Series		Accession: GSE83652	ID: 200083652

2896. Loss of Function Mutations in ETS2 Repressor Factor (ERF) Reveal a Balance Between Positive and Negative ETS Factors Controlling Prostate Oncogenesis [22PC RNA-seq]
(Submitter supplied) Half of prostate cancers are caused by a gene-fusion that enables androgens to drive expression of the normally silent ETS transcription factor ERG in luminal prostate cells1-4.  Recent prostate cancer genomic landscape studies5-10 have reported rare but recurrent point mutations in the ETS repressor ERF11.  Here we show these ERF mutations cause decreased protein stability and ERF mutant tumours are mostly exclusive from those with ERG fusions. 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/GSE83nnn/GSE83649/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326606
Series		Accession: GSE83649	ID: 200083649

2897. Primate Primordial Germ Cells Acquire Transplantation Potential by Carnegie Stage 23
(Submitter supplied) Primordial germ cells (PGCs) are the earliest embryonic progenitors in the germline. Correct formation of PGCs is critical to reproductive health as an adult. Recent work has shown that primate PGCs can be differentiated from pluripotent stem cells; however, a bioassay that supports their identity as transplantable germ cells has not been reported. Here, we adopted a xenotransplantation assay by transplanting single-cell suspensions of human and nonhuman primate embryonic Macaca mulatta (rhesus macaque) testes containing PGCs into the seminiferous tubules of adult busulfan-treated nude mice. more...
Organism:	Macaca mulatta; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Third-party reanalysis
Platform: GPL14954 10 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95736/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378239
Series		Accession: GSE95736	ID: 200095736

2898. AK144841 in Cutaneous Squamous Cell Carcinoma (cSCC)
(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: GPL16558 GPL16790 GPL13912 27 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89516/
Series		Accession: GSE89516	ID: 200089516

2899. Analysis of CAL165 cells transcriptome using RNASeq
(Submitter supplied) Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16558 1 Sample
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89510/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352418
Series		Accession: GSE89510	ID: 200089510

2900. Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2
(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 12 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98985/
Series		Accession: GSE98985	ID: 200098985

2901. Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 [RNA-seq]
(Submitter supplied) Over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). In this study, by manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, we identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 6 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98984/
Series		Accession: GSE98984	ID: 200098984

2902. Transcriptome analysis of MR1 reactive T cells
(Submitter supplied) MHC class I-related molecule MR1 presents riboflavin-derived microbial metabolites and folate-derivatives to mucosal-associated invariant T cells, but it is unknown whether MR1 can bind alternative antigens that stimulate other T cell lineages. Here we report that human T cells displaying diverse TCR-α and β chains recognize MR1-expressing cells in the absence of microbial ligands and respond to recombinant MR1 molecules loaded with antigens extracted from stimulatory targets. 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/GSE81nnn/GSE81063/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320397
Series		Accession: GSE81063	ID: 200081063

2903. SIRT7 Antagonizes TGF-β Signaling and Inhibits Breast Cancer Metastasis
(Submitter supplied) Protein deacetylase SIRT7 is significantly downregulated in lung metastases of human patient and mouse tissues, and predicted metastasis-free survival. To explore the roles of SIRT7 in breast cancer, we analysed the gene expressions in breast cancer BT549 cells with SIRT7 knockdown or not.
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/GSE99nnn/GSE99596/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388881
Series		Accession: GSE99596	ID: 200099596

2904. Gene Expression Analysis of Melanoma Cells Treated with 6-Thio-dG In Vitro
(Submitter supplied) Telomerase promoter mutations are highly prevalent in human tumors including melanoma. Telomere transcriptional signatures are enriched in a subset of therapy-naïve melanomas associated with worse overall survival, in BRAF-mutant intrinsically resistant melanoma cells that evade MAPK inhibitors (MAPKi), as well as in a subset of post-treatment tumor biopsies derived from patients who have disease progression on MAPKi or the immune checkpoint inhibitors, anti-CTLA-4 or anti-PD1. 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/GSE99nnn/GSE99552/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388966
Series		Accession: GSE99552	ID: 200099552

2905. JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC 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 6 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95592/
Series		Accession: GSE95592	ID: 200095592

2906. JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC cell lines [RNA-seq]
(Submitter supplied) The Epidermal Growth Factor Receptor (EGFR) regulates a diverse set of biological processes including cell growth, proliferation, and differentiation.  Deregulation of the EGFR pathway has been implicated in a variety of human diseases including cancer.  Gefitinib and erlotinib are tyrosine kinase inhibitors (TKIs) that have demonstrated clinical benefit for patients with Non-small cell lung cancer (NSCLC) and EGFR activating mutations. 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/GSE95nnn/GSE95558/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377575
Series		Accession: GSE95558	ID: 200095558

2907. Lipid Nanoparticle-Mediated Delivery of Anti-miR-17 Family Oligonucleotide Suppresses Hepatocellular Carcinoma Growth
(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: GPL11154 GPL570 16 Samples
FTP download: GEO (CEL, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93832/
Series		Accession: GSE93832	ID: 200093832

2908. mRNA Profiling of miR-17 family inhibition using TuD lentiviral vector in HepG2 and SK-Hep1 hepatocellular carcinoma cell lines [RNA-Seq]
(Submitter supplied) To functionally characterize the role of miR-17 family in HCC, lentiviral vector-based miR inhibitor TuD was used to inhibit miR-17 family of microRNAs in HepG2 and SK-Hep1 HCC cell lines
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/GSE93nnn/GSE93831/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362552
Series		Accession: GSE93831	ID: 200093831

2909. Gene expression profiling of KSHV-infected periodontal ligament cells
(Submitter supplied) We reported the potential and mechnism of oral mesenchymal stem cell to become Kaposi Sarcoma progenitor cell. Human periodontal ligament cells were infected for 48 hours and 96 hours, then subjected to RNA extraction and sequencing. We found that KSHV-infected PDLSC shared a better similarity with KS biosies in cytokine production, including chemotaxis, angiogenesis, inflammation and differentiation. 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/GSE92nnn/GSE92341/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358413
Series		Accession: GSE92341	ID: 200092341

2910. Next generation sequencing of esophageal squamous cell carcinoma (ESCC) cell line KYSE-180 single cell transcriptomes for radio-resistance analysis
(Submitter supplied) Purpose: Single cell RNA-seq could observe heterogeneity of cell transcriptomes. The goals of this study are to compare the changes of  ESCC cell line KYSE-180 RNA profiles in response to different doses of radiotherapy and to analyze the radio-resistance related genes.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 314 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81812/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322604
Series		Accession: GSE81812	ID: 200081812

2911. Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells.
(Submitter supplied) Nuclear factor TDP-43 is known to play an important role in several neurodegenerative pathologies. In general, TDP-43 is an abundant protein within the eukaryotic nucleus that binds to many coding and non-coding RNAs and influence their processing. Using Drosophila, we have performed a functional screening to establish the ability of major hnRNP proteins to affect TDP-43 overexpression/depletion phenotypes. more...
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/GSE97nnn/GSE97262/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381144
Series		Accession: GSE97262	ID: 200097262

2912. Capicua-dependent transcriptional changes in human cancer cell lines treated with trametinib
(Submitter supplied) We performed a genome-scale CRISPR screen in a KRAS-mutant pancreatic cancer cell line treated with the MEK inhibitor trametinib, and found that loss of the transcriptional repressor CIC confers resistance to MEK inhibition. We determined that CIC loss also confers resistance to MEK or BRAF inhibition in lung cancer, colorectal cancer, and melanoma cell lines with mutant RAS or BRAF. CIC is a transcriptional repressor that is phosphorylated and inhibited by the MAPK pathway. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 48 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE78nnn/GSE78519/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA313209
Series		Accession: GSE78519	ID: 200078519

2913. Human basal-like breast cancer cell line HCC1143 treated with BET inhibitor JQ1 in combination with MEK inhibitor Trametinib or PI3K/mTOR inhibitor BEZ235
(Submitter supplied) The goal of this experiment was to understand the changes in gene expression in the human basal-like breast cancer cell line HCC1143 following treatment with the MEK inhibitor Trametinib (T), PI3K/mTOR inhibitor BEZ235 (B), the BET inhibition JQ1 (JQ), Trametinib + JQ1 (TJ), or BEZ235 + JQ1(BJ), compared to a DMSO control (D). Samples were treated for 72hr and run in triplicate.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL11154 21 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE82nnn/GSE82032/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA323723
Series		Accession: GSE82032	ID: 200082032

2914. Hyper-repression of HUSH target genes by over-expression of the R252W Charcot-Marie-Tooth disease mutant MORC2
(Submitter supplied) By comparing wild-type SK-N-SH neuroblastoma cells to cells over-expressing either wild-type or R252W mutant MORC2, the goal of the experiment was to assess the effect of MORC2 over-expression on the transcriptome.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE95nnn/GSE95453/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA377250
Series		Accession: GSE95453	ID: 200095453

2915. Methylation DNA mediated KLF4 binding activity in glioblastoma cells
(Submitter supplied) RNA-seq, ChIP seq and Whole genome bisulfite seq for KLF4-mCpG binding in GBM cells
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 48 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382497
Series		Accession: GSE97632	ID: 200097632

2916. A comparison between single cell RNA sequencing and single molecule RNA FISH for rare cell analysis
(Submitter supplied) We use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ~2000 genes detected. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 801 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99330/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388108
Series		Accession: GSE99330	ID: 200099330

2917. Repurposing tofacitinib as an anti-myeloma therapeutic to reverse growth-promoting effects of the bone marrow microenvironment
(Submitter supplied) The myeloma bone marrow microenvironment promotes proliferation of malignant plasma cells and resistance to therapy. Interleukin-6 (IL-6) and downstream JAK/STAT signaling are thought to be central components of these microenvironment-induced phenotypes.  In a prior drug repurposing screen, we identified tofacitinib, a pan-JAK inhibitor FDA-approved for rheumatoid arthritis, as an agent that may reverse the tumor-stimulating effects of bone marrow mesenchymal stromal cells. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 3 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99293/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA388051
Series		Accession: GSE99293	ID: 200099293

2918. Splicing Modulators Act at the Branch Point Adenosine Binding Pocket Defined by the PHF5A-SF3b Complex
(Submitter supplied) Developing small-molecule splicing modulators represents a promising therapeutic approach for various diseases.  Natural products such as pladienolide, herboxidiene, and spliceostatin have been identified as potent splicing modulators that target SF3B1 in the SF3b subcomplex. Using integrated chemogenomic, structural and biochemical approaches, we show that PHF5A, another core component of the SF3b complex, is also targeted by these compounds. 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/GSE96nnn/GSE96917/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380104
Series		Accession: GSE96917	ID: 200096917

2919. Airway epithelial cells from high-risk subjects obtained via multiple bronchoscopy procedures to follow bronchial premalignant lesions as part of lung cancer screening
(Submitter supplied) While lung cancer is the leading cause of cancer death in the US, we have a limited understanding of the earliest molecular events preceding the onset of disease. Prior work has demonstrated that cigarette smoke creates a molecular “field of injury” throughout the airway epithelium and that there are distinct alterations in the airway transcriptome among smokers who have lung cancer. Molecular characterization of this airway “field of injury” in current and former smokers with premalignant lesions (PMLs) could provide novel insights into the earliest molecular events associated with lung carcinogenesis and identify relatively accessible biomarkers to guide lung cancer detection and early intervention. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 51 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79210/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315160
Series		Accession: GSE79210	ID: 200079210

2920. Airway epithelial cells from smokers with and without bronchial premalignant lesions
(Submitter supplied) While lung cancer is the leading cause of cancer death in the US, we have a limited understanding of the earliest molecular events preceding the onset of disease. Prior work has demonstrated that cigarette smoke creates a molecular “field of injury” throughout the airway epithelium and that there are distinct alterations in the airway transcriptome among smokers who have lung cancer. Molecular characterization of this airway “field of injury” in current and former smokers with premalignant lesions (PMLs) could provide novel insights into the earliest molecular events associated with lung carcinogenesis and identify relatively accessible biomarkers to guide lung cancer detection and early intervention. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 82 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79209/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA315161
Series		Accession: GSE79209	ID: 200079209

2921. Genome-wide analysis of AR binding and comparison with transcript expression in primary human fetal prostate fibroblasts and cancer associated fibroblasts
(Submitter supplied) We applied ChIPseq to identify genomic AR binding sites for the first time in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR. We identified AR binding sites that were specific to fetal prostate fibroblasts (7534), cancer fibroblasts (629), WPMY1-AR (2561) as well as those common among all (783). Primary fibroblasts had a distinct AR binding profile versus prostate cancer cell lines and tissue, and showed a localisation to gene promoter binding sites 1kb upstream of the transcriptional start site, as well as non-classical AR binding sequence motifs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform: GPL18573 7 Samples
FTP download: GEO (BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE90nnn/GSE90772/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA355876
Series		Accession: GSE90772	ID: 200090772

2922. Selective expression of long non-coding RNAs in a breast cancer cell progression model
(Submitter supplied) Long non-coding RNAs are emerging as key regulators of cancer cell activities. In this study, our goal was to perform a stringent profiling of breast cancer cell lines that represented a progression series. We used the MCF-10 series, which includes the normal-like MCF-10A, HRAS-transformed MCF-10AT1 (early-stage), and MCF-10CA1a (malignant). We have identified expressed mRNAs and lncRNAs within each cell type. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform: GPL18460 15 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98393/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384982
Series		Accession: GSE98393	ID: 200098393

2923. RNA-sequencing analysis of non silencing or ILF2 shRNA-transduced H929 cells
(Submitter supplied) To understand whether ILF2 is required to ensure the alternative splicing and processing of specific pre-mRNAs in Multiple Myeloma (MM) in physiological conditions, we performed RNA sequencing (RNA-Seq) analysis of ILF2-  and  non-silencing shRNA  transduced  H929 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/GSE97nnn/GSE97323/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381399
Series		Accession: GSE97323	ID: 200097323

2924. ILF2 Regulates RNA splicing of DNA Damage Response Genes to confer poor prognosis in 1q21-Amplified Multiple Myeloma
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 22 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83665/
Series		Accession: GSE83665	ID: 200083665

2925. RNA immunoprecipitation and sequencing of YB-1-bound transcripts in Multiple Myeloma
(Submitter supplied) To understand the mechanistic basis of YB-1’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. (RIP) and sequencing of YB-1-bound RNAs was performed in the JJN3 line (two biological replicates/condition).
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/GSE83nnn/GSE83664/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326672
Series		Accession: GSE83664	ID: 200083664

2926. RNA immunoprecipitation and sequencing of ILF2-bound transcripts in Multiple Myeloma
(Submitter supplied) To understand the mechanistic basis of ILF2’s regulation of mRNA splicing in response to DNA damage in Multiple Myeloma, we performed RNA immunoprecipitation (RIP) and sequencing of ILF2-bound transcripts under both physiological and DNA damage (melphalan treatment) conditions. Cells were treated with melphalan for 10 hours. RNA immunopreciptation (RIP) and sequencing of ILF2-bound RNAs was performed in the JJN3 and H929 cell lines (two biological replicates/condition). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 16 Samples
FTP download: GEO (DIFF) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83662/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326675
Series		Accession: GSE83662	ID: 200083662

2927. Gene expression profile of stage I lung adenocarcinoma and matched multi-site non-tumor lung samples
(Submitter supplied) In this study, a unique geographical tissue sampling collection was obtained from patients that underwent curative lobectomy for stage I pulmonary adenocarcinoma. Tumor and non-tumor lung samples located at 0, 2, 4, and 6 cm away from the tumor were collected. Whole genome gene expression profiling was performed on all samples (n = 5 specimens x 12 patients = 60). Analyses were carried out to identify genes differentially expressed in tumor compared to adjacent non-tumor lung tissues at different distances from the tumor as well as to identify stable and transient genes in non-tumor tissues with respect to tumor proximity.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL10558 57 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83213/
Series		Accession: GSE83213	ID: 200083213

2928. Targeting Taxane-Platin Resistant Lung Cancers with JumonjiC Lysine Demethylase 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
Platform: GPL11154 22 Samples
FTP download: GEO (BW) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81689/
Series		Accession: GSE81689	ID: 200081689

2929. Targeting Taxane-Platin Resistant Lung Cancers with JumonjiC Lysine Demethylase Inhibitors (RNA-Seq)
(Submitter supplied) Characterization of gene expression changes upon development of taxane-platin drug resistance in NSCLC cells and further, upon treatment of these resistant cells with the Jumonji KDM inhibitor, GSK-J4.
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/GSE81nnn/GSE81687/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA322315
Series		Accession: GSE81687	ID: 200081687

2930. Gene expression changes upon NUSAP1 over- or under-expression in PC-3 or DU145 cells.
(Submitter supplied) By transcriptome (RNA-Seq) analysis of PC-3 or DU145 prostate cancer cell lines over- or under-expressing NUSAP1, we determined genes that become differentially expressed upon expression changes of NUSAP1. Ingenuity Pathway Analysis revealed that the differentially expressed genes correlated with increased tumor progression and are involved in functions that include cancer, cellular movement, and cell morphology
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/GSE80nnn/GSE80963/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320286
Series		Accession: GSE80963	ID: 200080963

2931. CD133hi, Notchhi, DP (double positive) and DN (double negative) in GBML8 and GBML20, both patient-derived glioblastoma tumorsphere cultures
(Submitter supplied) CD133hi, Notchhi, DP and DN cells were FACS-isolated from GBML8 and GBML20 cultures and analyzed with RNA-seq, in order to find cell type-specific gene signatures. 
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/GSE99nnn/GSE99180/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA387469
Series		Accession: GSE99180	ID: 200099180

2932. Ets homologous factor has critical roles in epithelial dysfunction in airway disease
(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 21 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85403/
Series		Accession: GSE85403	ID: 200085403

2933. PHF20 readers link methylation of histone H3K4 and p53 with H4K16 acetylation
(Submitter supplied) PHF20 is a core component of the lysine acetyltransferase complex MOF-NSL that produces the major epigenetic mark, H4K16ac, and is necessary for transcriptional regulation and DNA repair, however the role of PHF20 in the complex remains elusive. Here, we report on functional crosstalk between epigenetic readers of PHF20. We show that the PHF20 PHD finger recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents first example of a native PHD reader selective for this modification. 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/GSE82nnn/GSE82115/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324082
Series		Accession: GSE82115	ID: 200082115

2934. YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction [RNA-seq]
(Submitter supplied) Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth retardation, feeding problems, and various congenital malformations. 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/GSE98nnn/GSE98476/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385185
Series		Accession: GSE98476	ID: 200098476

2935. Bromodomain protein BRD4 is a transcriptional repressor of autophagy and lysosomal function
(Submitter supplied) Autophagy is a membrane-trafficking process that directs degradation of cytoplasmic material in lysosomes. The process promotes cellular fidelity, and while the core machinery of autophagy is known, the mechanisms that promote and sustain autophagy are less well defined. Here we report that the epigenetic reader BRD4 and the methyltransferase G9a repress a TFEB/TFE3/MITF-independent transcriptional program that promotes autophagy and lysosome biogenesis. 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/GSE90nnn/GSE90444/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354629
Series		Accession: GSE90444	ID: 200090444

2936. Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics
(Submitter supplied) Ribosome profiling is a widespread tool for studying translational dynamics in human cells.  Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis.  Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics.  We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 12 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE69nnn/GSE69047/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA284399
Series		Accession: GSE69047	ID: 200069047

2937. Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing
(Submitter supplied) Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on single T cells isolated from peripheral blood, tumor and adjacent normal tissues from hepatocellular carcinoma patients.
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/GSE98nnn/GSE98638/
Series		Accession: GSE98638	ID: 200098638

2938. Chromatin states of tumor-specific T cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 97 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89309/
Series		Accession: GSE89309	ID: 200089309

2939. Transcriptome analysis of CNS leukemia
(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: GPL16791 GPL14550 16 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE81nnn/GSE81519/
Series		Accession: GSE81519	ID: 200081519

2940. RNA-seq analysis of primary patient samples to characterize the CNS leukemia
(Submitter supplied) We present a detailed genetic, transcriptional and physiological study of leukemic cells isolated from the CNS and bone marrows (BM) of both affected children and xenograft model of B-ALL which recapitulate the key features of CNS involvement. We reveal that leukemic cells in CNS possess distinct hypoxic signature such as proliferation suppression, decrease of mitochondrial oxidative phosphorylation and increase of glycolysis compared with leukemic cells in BM.
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/GSE81nnn/GSE81518/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321847
Series		Accession: GSE81518	ID: 200081518

2941. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
(Submitter supplied) Single-cell whole transcriptome analysis of  chronic myeloid leukemia stem cells, defined as Lin-CD34+CD38-.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL20301 GPL11154 2289 Samples
FTP download: GEO (RDATA, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76312/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA306878
Series		Accession: GSE76312	ID: 200076312

2942. Transcriptome analysis in HT29 and SW480 cells depleted of Prdx2
(Submitter supplied) Prdx2 is the thioredoxin-dependent peroxidase that reduces H2O2 using reducing power NADPH in the presence of thioredoxin and thioredoxin reductase. Prdx2 plays an important role in growth. factor signaling in mammlian cells. Therefore, we examined the gene expression in colon adenocarcinoma cell line HT29 after Prdx2 depletion. Prdx2 depletion resulted in a significant alteration on gene expression, including protein synthesis, metabolisms, and cell cycle.
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/GSE81nnn/GSE81429/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321515
Series		Accession: GSE81429	ID: 200081429

2943. Circadian networks in human embryonic stem cell-derived cardiomyocytes
(Submitter supplied) Cell-autonomous circadian oscillations strongly influence tissue physiology and pathophysiology of peripheral organs. Recent in vivo findings in the heart demonstrate that the circadian clock controls oscillatory gene expression programs in the adult myocardium. However, whether in vitro human embryonic stem (ES) cell-derived cardiomyocytes can establish circadian rhythmicity is unknown. Here we report that while undifferentiated human ES cells do not possess a functional clock, oscillatory expression of known core clock genes emerges during directed cardiac differentiation, with robust rhythms in day 30 cardiomyocytes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18573 4 Samples
FTP download: GEO (RTF, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97142/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA381615
Series		Accession: GSE97142	ID: 200097142

2944. A practical solution for preserving single cells for RNA sequencing
(Submitter supplied) We present a method for histological tissue fixation using dithio-bis(succinimidyl propionate) (DSP), or Lomant's Reagent, to stabilise cell samples for single-cell transcriptomic applications.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL20301 267 Samples
FTP download: GEO (TXT, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98734/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA386155
Series		Accession: GSE98734	ID: 200098734

2945. ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator [RNA-seq]
(Submitter supplied) Here we show that ZBTB48 binds directly both to telomeric as well as to subtelomeric variant repeat sequences. ZBTB48 is found at telomeres of human cancer cells regardless of the mode of telomere maintenance and it acts as a negative regulator of telomere length. In addition to its telomeric function, we demonstrate through a combination of RNAseq, ChIPseq and expression proteomics experiments that ZBTB48 acts as a transcriptional activator on a small set of target genes, including mitochondrial fission process 1 (MTFP1). 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/GSE96nnn/GSE96777/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379623
Series		Accession: GSE96777	ID: 200096777

2946. CRISPR/Cas9 Screens Reveal Epstein-Barr virus Synthetic Lethal Targets
(Submitter supplied) Epstein-Barr virus (EBV) causes endemic Burkitt lymphoma and immunosuppression-related lymphomas.  These B-cell malignancies arise by distinct transformation pathways and utilize divergent viral and host expression programs.  To identify host dependency factors elicited by EBV latent-infection states, we performed parallel genome-wide CRISPR/Cas9 screens in Burkitt lymphoma (BL) and lymphoblasotid cell lines (LCL). 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/GSE93nnn/GSE93681/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA361554
Series		Accession: GSE93681	ID: 200093681

2947. POLR3G Dependent PolyA+ and smallRNA Transcriptomes in Human Pluripotent Stem Cells
(Submitter supplied) POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms, which are not known in detail. In order to explore how POLR3G regulates stem cell state, we have carried out deep sequencing analysis of polyA+ and smallRNA transcriptomes present in hPSCs and regulated in POLR3G dependent manner. Our data reveals that POLR3G regulates a specific subset of the hPSC transcriptome, including multiple transcripts types, such as protein coding genes, lincRNAs, miRNAs and snoRNAs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms: GPL11154 GPL21290 18 Samples
FTP download: GEO (BED, BIGWIG, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94696/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA371846
Series		Accession: GSE94696	ID: 200094696

2948. Genes that mediate leptomeningeal metastasis from breast and lung solid tumor primaries
(Submitter supplied) Little is understood about the gene expression changes that underlie cancer spread to the cerebrospinal fluid, or leptomeningeal metastasis. Using four cancer cell line models, we empolyed iterative in vivo selection to generate subpopulations of these cell lines able to access the leptomeningeal space and grow once there. We compared the gene expression profile of the terminally selected cells or "Lep" cells with that of the parental or "Par" cells, as well as that of an intermediate stage of in vivo selection or "Int" cells. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL13112 GPL11154 41 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83132/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA324845
Series		Accession: GSE83132	ID: 200083132

2949. Human RELA haploinsufficiency results in autosomal dominant chronic mucocutaneous ulceration: the transcriptional profile of RelA haploinsufficient patients
(Submitter supplied) The treatment of chronic mucocutaneous ulceration is challenging and only some patients respond selectively to inhibitors of tumor necrosis factor-alpha (TNF-a). TNF-a activates opposing pathways leading to caspase-8-mediated apoptosis as well as NF-kB-dependent cell survival. We investigated the etiology of autosomal dominant mucocutaneous ulceration in a family whose proband was dependent on anti-TNF-a therapy for sustained remission. 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/GSE98nnn/GSE98624/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385770
Series		Accession: GSE98624	ID: 200098624

2950. Interferon receptor signaling pathways regulating PD-L1 and PD-L2 expression
(Submitter supplied) We studied the molecules involved in downstream signaling induced by interferons to regulate PD- L1 and PD-L2 expression using a shRNA screen, Western blot, mRNAexpression profiling, promoter truncation analysis and chromatin immunoprecipitation.These studies revealed that the interferon gamma-JAK1/2-STAT1-IRF1 axis primarily regulates PD-L1 expression, with IRF1 binding to its promoter. PD-L2 responded equally to interferon beta and gamma, and shared regulation through IRF1 and alsoSTAT3, which bind to the PD-L2 promoter. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 10 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96619/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379183
Series		Accession: GSE96619	ID: 200096619

2951. 12hr 5-FU treatment vs. DMSO in SJSA cells (from 'A kinase independent role for CDK19 in p53 response')
(Submitter supplied) The human Mediator complex regulates RNA Polymerase II transcription genomewide. A general factor that regulates Mediator function is the four-subunit Mediator kinase module, which contains either CDK8 or CDK19. Whereas CDK8 has been linked to specific signaling cascades and oncogenesis, the cellular roles of its paralog, CDK19, are poorly studied. To define cellular roles for CDK19, we used osteosarcoma cells (SJSA) that naturally lack endogenous CDK8 protein. 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/GSE89nnn/GSE89807/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA353364
Series		Accession: GSE89807	ID: 200089807

2952. Gene expression of  thyroid cancer cell lines
(Submitter supplied) Purpose: The primary goal of this study was to identify gene-expression profiles of  anaplastic thyroid cancer and  to identify some novel in-frame gene fusions that could result in translated protein products affecting the development of  anaplastic thyroid cancer. Methods: RNAseq Data was processed with TCGA UNC V2 RNAseq protocol and different expressed genes were identify by using DESeq2, limma-voom, and edgeR. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 11 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94464/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369782
Series		Accession: GSE94464	ID: 200094464

2953. Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses
(Submitter supplied) We perform massively parallel single cell RNA-seq (MARS-Seq) on non-lymphocytic immune cells sorted from a human stage IA lung adenocarcinoma lesion and from the adjacent non-involved lung. With an unbiased single cell transcriptomic analysis of non-lymphocyte cells accumulating in these tissues, we sought to capture the heterogeneity of the tumor-infiltrating myeloid (TIM) compartment. Using a previously described unbiased expectation-maximization algorith (Paul et al., 2015), we identified clusters that were then named according to literature-reported marker profiles. 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/GSE97nnn/GSE97168/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380875
Series		Accession: GSE97168	ID: 200097168

2954. Expression profiling of MCF-7 cells with treatment of TCDD
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98515/
Series		Accession: GSE98515	ID: 200098515

2955. Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation
(Submitter supplied) We set out to identify molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes. Gene expression changes unequivocally discriminated benign versus malignant states, and a dual epigenetic and immune signature emerged defining this transition. We discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was discriminated by a 122-epigenetic gene signature (‘epigenetic’ cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 78 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98394/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA385075
Series		Accession: GSE98394	ID: 200098394

2956. High-purity circular RNA isolation method (RPAD) reveals vast collection of intronic circRNAs (IcircRNAs)
(Submitter supplied) High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin, and functions are largely unknown.  Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs. more...
Organism:	Mus musculus; Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL17021 GPL16791 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92632/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358203
Series		Accession: GSE92632	ID: 200092632

2957. Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Human gammaherpesvirus 8; Homo sapiens
Type:		Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms: GPL19367 GPL11154 15 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91386/
Series		Accession: GSE91386	ID: 200091386

2958. Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling (mRNA)
(Submitter supplied) Virus-like vesicles (VLVs) are membrane derived cellular vesicles that resemble native envelope viruses in organization and conformation, but lack viral capsid and/or genome. During productive virus infection, both infectious virions and non-infectious VLVs are produced and released into the extracellular space. VLVs have been shown to play a role in intercellular communication and in facilitating virus infection. more...
Organism:	Homo sapiens; Human gammaherpesvirus 8
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL19367 14 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE91nnn/GSE91384/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA356918
Series		Accession: GSE91384	ID: 200091384

2959. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis
(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; Methylation profiling by high throughput sequencing; Other
6 related Platforms 863 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87064/
Series		Accession: GSE87064	ID: 200087064

2960. The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Hs]
(Submitter supplied) In the developing retina, as in many other regions of the central nervous system, multipotent neural progenitor cells undergo unidirectional changes to produce differentiated cells in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinal development in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell type–specific differentiation programs. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL16791 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE87nnn/GSE87042/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA343264
Series		Accession: GSE87042	ID: 200087042

2961. MicroRNA-28 replacement for non-Hodgkin lymphoma therapy
(Submitter supplied) Our studies identify the role of mIR-28 in germinal center response and its therapeutic potential for the treatment of non-Hodgkin lymphomas
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/GSE81nnn/GSE81236/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA321033
Series		Accession: GSE81236	ID: 200081236

2962. Silencing of KDM2B leads to deregulation of apoptosis related genes in GBM
(Submitter supplied) Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising anti-cancer protein that can specifically kill tumor cells while sparing healthy ones. Emerging evidences suggest that TRAIL resistance in cancers is associated with aberrant expression of the key components of the apoptotic program. However, how these components are regulated at the epigenetic level is not understood. In this study, we aimed to identify novel epigenetic mechanisms regulating TRAIL response in Glioblastoma Multiforme (GBM) by a short-hairpin RNA (shRNA) screen. more...
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/GSE81nnn/GSE81043/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320464
Series		Accession: GSE81043	ID: 200081043

2963. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (Leukemia Cell Bank)
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. more...
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/GSE72nnn/GSE72061/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292885
Series		Accession: GSE72061	ID: 200072061

2964. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (RNA-seq AML development)
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. 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/GSE71nnn/GSE71800/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA292133
Series		Accession: GSE71800	ID: 200071800

2965. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets [RNA-Seq_normal]
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. 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/GSE71nnn/GSE71689/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291824
Series		Accession: GSE71689	ID: 200071689

2966. Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets [RNA-Seq_AML]
(Submitter supplied) Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. 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/GSE71nnn/GSE71686/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA291825
Series		Accession: GSE71686	ID: 200071686

2967. Inhibiting the oncogenic translation program is an effective therapeutic strategy in multiple myeloma
(Submitter supplied) Multiple Myeloma (MM) is a frequently incurable hematological cancer in which over activity of MYC plays a central role, notably through upregulation of ribosome biogenesis and translation. To better understand the oncogenic program driven by MYC and investigate its potential as a therapeutic target, we screened a chemically diverse small molecule library for anti-MM activity. The most potent hits identified were rocaglate-scaffold inhibitors of translation initiation. 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/GSE94nnn/GSE94827/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA374537
Series		Accession: GSE94827	ID: 200094827

2968. Acquired resistance mechanisms to capmatinib, a MET inhibitor in MET-amplified non-small cell lung cancer cells
(Submitter supplied) Purpose: MET is a receptor tyrosine kinase (RTK) that has been considered a druggable target in non-small cell lung cancer (NSCLC). To understand the mechanisms of resistance to MET-TKIs and establish therapeutic strategies, we developed an in vitro model using capmatinib-resistant cell lines (EBC-CR1, CR2, and CR3) derived from the MET-amplified NSCLC cell line EBC-1. Methods: We established capmatinib-resistant NSCLC cell lines from the MET-amplified NSCLC cell line EBC-1 and identified alternative signaling pathways using 3’mRNA sequencing and human phospho-RTK arrays. 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/GSE94nnn/GSE94405/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369611
Series		Accession: GSE94405	ID: 200094405

2969. Identification of target genes of TAZ in the prostate cancer cells
(Submitter supplied) We found that the transcriptinal co-activator TAZ is a basal cell marker for the prostate epithelium which is lost in the prostate cancer tissues and re-expression of TAZ in the prostate cancers may be a indicator of malignancy. TAZ promotes cell migraiton, EMT and metastasis in the prostate cancers. To elucidate the underlying mechanism, we performed the RNA-seq analysis of TAZ knockdown DU145 cells using two independent TAZ shRNA and pLKO control cells.
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/GSE93nnn/GSE93748/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362294
Series		Accession: GSE93748	ID: 200093748

2970. Gene expression profile of human multiple myeloma cell line MM.1S after knockdown of KDM6B
(Submitter supplied) Recent studies have delineated cancer type-specific roles of histone 3 lysine 27 (H3K27) demethylase KDM6B/JMJD3 depending on its H3K27 demethylase activity. Here we show that KDM6B is expressed in multiple myeloma (MM); and that shRNA-mediated knockdown and CRISPR-mediated knockout of KDM6B abrogate MM cell growth and survival. TNFα or bone marrow stromal cell culture supernatants induce KDM6B, which is blocked by IKKβ inhibitor MLN120B, suggesting KDM6B is regulated by NF-κB signaling in MM 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/GSE93nnn/GSE93395/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA360859
Series		Accession: GSE93395	ID: 200093395

2971. Gene expression profile of melanoma cell lines after overexpression or knockdown of KPC1
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 12 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79113/
Series		Accession: GSE79113	ID: 200079113

2972. Transcriptome analysis of G protein-coupled receptors in distinct genetic subgroups of acute myeloid leukemia: identification of potential disease-specific targets
(Submitter supplied) Acute myeloid leukemia (AML) is associated with poor clinical outcome and the development of more effective therapies is urgently needed. G protein-coupled receptors (GPCRs) represent attractive therapeutic targets, accounting for approximately 30% of all targets of marketed drugs. Using next-generation sequencing, we studied the expression of 772 GPCRs in 148 genetically diverse AML specimens, normal blood and bone marrow cell populations as well as cord blood-derived CD34-positive cells. 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/GSE98nnn/GSE98310/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA384650
Series		Accession: GSE98310	ID: 200098310

2973. Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma
(Submitter supplied) We performed transcriptome sequencing for hepatocellular carcinoma (HCC) and adjacent non-tumorous tissues to investigate the molecular basis of HCC. Nine HCC patients were recruited and differentially expressed genes (DEGs) were identified. Candidate fusion transcripts were also identified. Further RT-PCR and Sanger sequencing experiments were performed to validate potential recurrent fusion transcripts in other 54 pairs of tumor and adjacent non-tumor samples. 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/GSE97nnn/GSE97214/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA380984
Series		Accession: GSE97214	ID: 200097214

2974. Genome-wide analysis of DNA hydroxymethylation and methylation during epstein-barr virus infection.
(Submitter supplied) Extensive DNA methylation in promoter regions is observed in gastric cancer with Epstein-barr virus (EBV) infection and EBV infection is the cause to induce this extensive hypermethylaiton phenotype in gastric epithelial cells. From transcriptome analysis, we found that TET2, one of the demethylase enzymes, was downregulated by EBV infection in gastric epithelial cell line MKN7. TET2 was overexpressed in a gastric epithelial cell line, GES1, to see its function and the hydroxymethylation, a byproduct of DNA demethylation, acquired genes by TET2 overexpression and methylation acquired genes by EBV infection were significantly overlapped. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms: GPL18460 GPL18573 8 Samples
FTP download: GEO (BIGWIG, GTF, XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE84nnn/GSE84897/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA335645
Series		Accession: GSE84897	ID: 200084897

2975. Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma
(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: GPL11154 GPL18573 80 Samples
FTP download: GEO (BED, BEDGRAPH, FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83728/
Series		Accession: GSE83728	ID: 200083728

2976. PAX3-FOXO1 requires BRD4 to drive oncogene addiction in RMS cells [RNA-seq]
(Submitter supplied) The fusion transcription factor PAX3-FOXO1 drives oncogenesis in a subset of rhabdomyosarcomas, however the mechanisms by which it remodels chromatin are unknown.  We find PAX3-FOXO1 reprograms the cis-regulatory landscape by inducing super enhancers (SEs), in collaboration with master transcription factors MYOG, MYOD and MYCN.  This myogenic SE circuitry is consistent across cell lines and primary tumors. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platforms: GPL11154 GPL18573 10 Samples
FTP download: GEO (FPKM_TRACKING) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE83nnn/GSE83724/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA326875
Series		Accession: GSE83724	ID: 200083724

2977. Gene expression profile in IM-0223 cells transfected with KPC1 or control vector using RNA-seq
(Submitter supplied) Melanoma is a highly aggressive cancer with increasing incidence rates and a poor survival, particularly in patients with AJCC stage IV and advanced stage III. Deregulation of NF-kB is linked to different pathological states, including melanoma. To identify the involvement of NF-kB pathway regulation in melanoma progression, we manipulated NF-kB pathway activation and profiled gene expression using RNA-sequencing.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 4 Samples
FTP download: GEO (CSV, TAB) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE79nnn/GSE79111/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA314972
Series		Accession: GSE79111	ID: 200079111

2978. List of TIAM1 differentially expressed genes in SW620 cells [RNA-seq]
(Submitter supplied) The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange factor (GEF) that activates the small GTPase RAC1 and regulates a plethora of functions such as cell proliferation, migration, apoptosis and polarity. Recently, we demonstrated that TIAM1 shuttles between the cytoplasm and nucleus. To determine the nuclear role of TIAM1, we performed RNA-seq on SW620 cells transfected either with a specific pre-validated siRNA for TIAM1 (siTIAM1) or a negative control siRNA (siNT) and generated a list of TIAM1 differentially expressed genes. 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/GSE90nnn/GSE90491/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA354872
Series		Accession: GSE90491	ID: 200090491

2979. RNA sequencing of erythroid and granulomonocytic colonies differentiated from transduced bone marrow CD34+ cells expressing U2AF1 S34F mutation, U2AF1 wild-type or empty vector control
(Submitter supplied) Mutations of the splicing factor U2AF1 are frequent in the myeloid malignancy myelodysplastic syndromes (MDS) and in other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and increasing bone marrow blasts. We investigated the impact of the common U2AF1 S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1 S34F expression in human hematopoietic progenitors impairs erythroid differentiation, and skews granulomonocytic differentiation towards granulocytes. 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/GSE94nnn/GSE94153/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369090
Series		Accession: GSE94153	ID: 200094153

2980. Lysine-specific demethylase 1 metastasis of androgen-independent PCa 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: GPL11154 6 Samples
FTP download: GEO (TXT, WIG) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57079/
Series		Accession: GSE57079	ID: 200057079

2981. Lysine-specific demethylase 1 metastasis of androgen-independent PCa cells [RNA-seq]
(Submitter supplied) The aim of this study is to identify the LSD1 target genes in metastatic androgen independent prostate cancer Lysine-specific demethylase 1 (LSD1) was shown to control gene expression and cell proliferation of androgen-dependent prostate cancer (PCa) cells, whereas the role of LSD1 in androgen-independent metastatic prostate cancer remains elusive. Here, we show that depletion of LSD1 leads to increased migration and invasion of androgen-independent PCa cells. 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/GSE57nnn/GSE57078/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA245397
Series		Accession: GSE57078	ID: 200057078

2982. Transcriptional profiles of CD8+ T cells from peripheral blood of melanoma patients before and after anti-PD1 therapy
(Submitter supplied) RNA-Seq analysis was used to study the profile of CD8 t cells from melanoma patients before and after treatment to understand if we can detect transcriptional changes in peripheral blood
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL23177 13 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96578/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA378793
Series		Accession: GSE96578	ID: 200096578

2983. Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL16791 13 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93653/
Series		Accession: GSE93653	ID: 200093653

2984. Transcriptional dependencies in diffuse intrinsic pontine glioma
(Submitter supplied) Diffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor with limited therapeutic options. The majority of cases of DIPG exhibit a mutation in histone 3 (H3K27M) that results in oncogenic transcriptional aberrancies. We show here that DIPG is vulnerable to transcriptional disruption using either bromodomain inhibition or CDK7 blockade. We observe that targeting oncogenic transcription through either of these methods synergizes with HDAC inhibition and that DIPG cells resistant to HDAC inhibitor therapy retain sensitivity to CDK7 blockade. more...
Organism:	Homo sapiens
Type:		Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms: GPL18573 GPL20301 26 Samples
FTP download: GEO (BW, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94259/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA369207
Series		Accession: GSE94259	ID: 200094259

2985. Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy
(Submitter supplied) Ion channels and transporters have increasingly recognized roles in cancer progression through the regulation of cell proliferation, migration, and death. Glioblastoma stem-like cells (GSCs) are a source of tumor formation and recurrence in glioblastoma multiforme, a highly aggressive brain cancer, suggesting that ion channel expression may be perturbed in this population. However, little is known about the expression and functional relevance of ion channels that may contribute to GSC malignancy. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 69 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89623/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA352731
Series		Accession: GSE89623	ID: 200089623

2986. Perturbation-response genes reveal signaling footprints in cancer gene expression
(Submitter supplied) Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Here we present PROGENy, a method that overcomes both limitations by leveraging a large compendium of publicly available perturbation experiments to yield a common core of Pathway RespOnsive GENes. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 24 Samples
FTP download: GEO (TSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97979/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA383562
Series		Accession: GSE97979	ID: 200097979

2987. Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties
(Submitter supplied) Characterization of non-neoplastic and malignant human stem cell populations in their native state can provide new insights into gliomagenesis. Here we developed a purification strategy to directly isolate EGFR+/– populations from human germinal matrix (GM) and adult subventricular zone autopsy tissues, and from de-novo glioblastoma (GBM) resections, enriching for cells capable of binding EGF ligand (LBEGFR+), and uniquely compared their functional and molecular properties. 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/GSE96nnn/GSE96682/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA379363
Series		Accession: GSE96682	ID: 200096682

2988. DDX54 regulates transcriptome dynamics during DNA damage response
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platform: GPL11154 33 Samples
FTP download: GEO (BED, TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE89nnn/GSE89369/
Series		Accession: GSE89369	ID: 200089369

2989. DDX54 regulates transcriptome dynamics during DNA damage response [RNA-seq2]
(Submitter supplied) The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of posttranscriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing irradiation (IR). 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/GSE89nnn/GSE89368/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA351888
Series		Accession: GSE89368	ID: 200089368

2990. DDX54 regulates transcriptome dynamics during DNA damage response [RNA-seq1]
(Submitter supplied) The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of posttranscriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing irradiation (IR). 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/GSE89nnn/GSE89367/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA351889
Series		Accession: GSE89367	ID: 200089367

2991. DDX54 regulates transcriptome dynamics during DNA damage response [4SU-seq]
(Submitter supplied) The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of posttranscriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing irradiation (IR). 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/GSE89nnn/GSE89365/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA351887
Series		Accession: GSE89365	ID: 200089365

2992. Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients
(Submitter supplied) Purpose: To identify transcriptional changes by RNA-seq in tumor samples, before bevacizumab combination treatment and after bevacizumab combination treatment in both responding and non-responding recurrent glioblastoma patients
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/GSE79nnn/GSE79671/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA316676
Series		Accession: GSE79671	ID: 200079671

2993. 5-methylcytosine promotes mRNA export
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
4 related Platforms 44 Samples
FTP download: GEO ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93751/
Series		Accession: GSE93751	ID: 200093751

2994. Transcriptomics of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues
(Submitter supplied) RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. more...
Organism:	Homo sapiens; Mus musculus
Type:		Expression profiling by high throughput sequencing
Platforms: GPL16791 GPL21493 GPL21290 22 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93750/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA362513
Series		Accession: GSE93750	ID: 200093750

2995. Gastric cancer targeted RNA-seq
(Submitter supplied) targeted gene sequencong of 157 preselected genes in upper GI biopsies and resected stomack tissues
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 110 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80389/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318782
Series		Accession: GSE80389	ID: 200080389

2996. Gastric cancer RNA-seq
(Submitter supplied) RNA  sequencong of 9 upper GI gastric biopsies and resected gastric tissues
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL15520 9 Samples
FTP download: GEO (XLSX) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80388/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA318783
Series		Accession: GSE80388	ID: 200080388

2997. Evolving Spindlin1 Small Molecule Inhibitors Using Protein Microarrays
(Submitter supplied) Using a library of tagged UNC1215 analogs, we screened a protein domain microarray of methyl-lysine effector molecules to rapidly detect compounds with novel binding profiles. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor domain-containing protein Spindlin1 (SPIN1). Structural studies revealed that the symmetric nature of EML405 allows it to simultaneously engage two of SPIN1’s Tudor domains, and also facilitated the rational synthesis of more selective SPIN1 inhibitor (EML631). more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL16791 9 Samples
FTP download: GEO (XLS) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92547/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA358011
Series		Accession: GSE92547	ID: 200092547

2998. Runx1 stabilizes the mammary epithelial cell phenotype and prevents epithelial to mesenchymal transition
(Submitter supplied) The Runx1 transcription factor is essential for hematopoietic differentiation and mutations underlie various leukemias. Here we demonstrate a role for Runx1 in the MCF10 cell series model of breast cancer progression. The highest level of Runx1 that occurs in normal like mammary epithelial cells (MCF10A) is decreased in tumorigenic (MCF10AT1) and metastatic (MCF10CA1a) breast cancer cells. We show that depletion of Runx1 in MCF10A cells results in striking changes in cell morphology and induction of epithelial-mesenchymal transition (EMT) via several signaling pathways. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL18460 6 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE85nnn/GSE85857/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA339558
Series		Accession: GSE85857	ID: 200085857

2999. Cooperativity between EMT and non-EMT cells promotes breast cancer metastasis via paracrine GLI activation
(Submitter supplied) Recent fate mapping studies concluded that EMT is not required for metastasis of carcinomas. Here we challenge this conclusion by showing that it failed to account for possible crosstalk between EMT and non-EMT cells that promotes dissemination of non-EMT cells. In breast cancer models, EMT cells induce increased metastasis of weakly metastatic, non-EMT tumor cells in a paracrine manner in part by non-cell autonomous activation of the GLI transcription factor. more...
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing
Platform: GPL11154 36 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97726/
SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA382735
Series		Accession: GSE97726	ID: 200097726

3000. Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance
(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 155 Samples
FTP download: GEO (BEDGRAPH) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE97nnn/GSE97682/
Series		Accession: GSE97682	ID: 200097682

