GPL9442[RGSE] - GEO DataSets

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Select item 2001522311.

Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases

(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 GPL9442
27 Samples

Download data: BED

Series

Accession:: GSE152231

ID:: 200152231

PubMed Full text in PMC Similar studies

Select item 2001522302.

Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases [RNA-seq]

(Submitter supplied) We performed transcriptional profiling and chromatin immunoprecipitation for the key oncogenic driver in prostate cancer, Androgen Receptor (AR) and FOXA1, H3K27ac, H3K27me3 and CTCF to chart the epigenomic landscape in four clonal metastatic tumors from a single prostate cancer patient whose clinical course was closely followed over 17 years. The vast majority (~80% ) of all AR binding sites were shared among all samples and found in normal prostate tissue and primary prostate cancers signifying core binding events within the prostate lineage. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9442
4 Samples

Download data: TXT

Series

Accession:: GSE152230

ID:: 200152230

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001087733.

Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome

(Submitter supplied) Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL18573 GPL9442
8 Samples

Download data: BW

Series

Accession:: GSE108773

ID:: 200108773

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000749434.

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

Download data: TXT

Series

Accession:: GSE74943

ID:: 200074943

PubMed Full text in PMC Similar studies

Select item 2000749425.

Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast cancer [Methyl-MAPS]

(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:: Methylation profiling by high throughput sequencing

Platform:: GPL9442
4 Samples

Download data: TXT

Series

Accession:: GSE74942

ID:: 200074942

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000675556.

TFAP2A ChIP-seq in human primary melanocytes

(Submitter supplied) Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9442
2 Samples

Download data: BED

Series

Accession:: GSE67555

ID:: 200067555

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000868387.

Genome-wide positioning of bivalent mononucleosomes

(Submitter supplied) Background: Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9442
5 Samples

Download data: BED, TXT

Series

Accession:: GSE86838

ID:: 200086838

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000844578.

Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus; Homo sapiens

Type:: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9318 GPL4134 GPL9442
14 Samples

Download data: TXT, WIG

Series

Accession:: GSE84457

ID:: 200084457

Select item 2000844569.

Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts [ChIP-seq]

(Submitter supplied) Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector β-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. more...

Organism:: Mus musculus; Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9318 GPL9442
6 Samples

Download data: WIG

Series

Accession:: GSE84456

ID:: 200084456

PubMed Similar studies

Select item 20008103210.

Comparative proteomics and transcriptomics study of signaling network proteins across multiple normal and cancer cell lines

(Submitter supplied) It is not known whether cancer cells generally show quantitative differences in the expression of signaling pathway proteins that could dysregulate signal transduction. To explore this issue, we first defined the primary components of the EGFR-MAPK pathway in normal human mammary epithelial cells, identifying 16 core proteins and 10 feedback regulators. We then quantified their absolute abundance at both the protein and mRNA level across a panel of normal and breast cancer cell lines. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9442
7 Samples

Download data: TXT

Series

Accession:: GSE81032

ID:: 200081032

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20006247211.

Cell context specific effect of AR antagonists on AR DNA binding and target gene expression

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens; Mus musculus

Type:: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms
68 Samples

Download data: BED

Series

Accession:: GSE62472

ID:: 200062472

Analyze with GEO2R

Select item 20006244212.

Androgen receptor DNA binding in response to different ligands across three prostate cancer cell lines

(Submitter supplied) We performed AR ChIP-seq in LNCaP-AR, VCaP and CWR22PC cells in the presence of vehicle, androgen, or androgen plus antiandrogen. These three cell lines showed variable sensitivity to these drugs.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9442 GPL11154
15 Samples

Download data: BED

Series

Accession:: GSE62442

ID:: 200062442

SRA Run Selector

Select item 20006641213.

RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.

(Submitter supplied) The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. In this project we used SOLiD next generation sequencing to characterize gene expression profiles in normal human epidermal keratinocytes (NHEKs) and cSCC cell lines.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9442
12 Samples

Download data: TXT

Series

Accession:: GSE66412

ID:: 200066412

PubMed Similar studies SRA Run Selector

Select item 20005517214.

Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs

(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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL9442 GPL11154
21 Samples

Download data: BEDGRAPH, BW

Series

Accession:: GSE55172

ID:: 200055172

PubMed Full text in PMC Similar studies

Select item 20005516915.

Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (RNA-Seq)

(Submitter supplied) Oxidative stress (OS) is caused by an imbalance between pro-oxidant and antioxidant reactions which leads to accumulation of reactive oxygen species (ROS) within cells. ROS can be harmful, due to their damaging effects on several cellular components, but are at the same time essential components of signaling cues. We investigate the effect of OS on the immediate early transcriptional response at a genomic level, by deep sequencing of nuclear and cytosolic RNA fractions, in in human fibroblasts treated for 30 or 120 minutes with sub-lethal doses of H2O2. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9442
12 Samples

Download data: BW

Series

Accession:: GSE55169

ID:: 200055169

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003570416.

Whole Transcriptome RNA-seq Analysis: the Tumorigenesis and Metastasis of Melanoma

(Submitter supplied) To better understand the tumorigenesis and metastasis of human metastatic melanoma(MM) , we analyzed the transcriptomes of three cell lines that represent the three distinct stages of MM pathogenesis: the normal stage (HEMn), the onset of MM (A375), and the metastasis stage (A2085). Using the next generation sequencing (NGS) technology, we detected unsymmetrical expression of genes particularly in Chr9, 12, and 14 among three cell lines, an indication of the involvement of these genes in the tumorigenesis and metastasis of MM. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9442
3 Samples

Download data: WIG

Series

Accession:: GSE35704

ID:: 200035704

PubMed Similar studies SRA Run Selector

Select item 20005840617.

NOTCH1 ChIP-Seq in HBPALL cell lines

(Submitter supplied) ChIP-Seq detected global binding of NOTCH1 oncogene in a human T-Cell Leukemia Cell line.

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9442
2 Samples

Download data: BED, BEDGRAPH

Series

Accession:: GSE58406

ID:: 200058406

PubMed Full text in PMC Similar studies

Select item 20005143018.

Genome sequencing coupled with iPSC technology identifies GTDC1 as a novel candidate gene involved in Neurodevelopmental Disorders

(Submitter supplied) We identified genomic structural alterations of six patients with signs of neurodevelopmental disorder (NDDs) that harbour chromosomal rearrangements using large-insert paired-end tag sequencing (DNA-PET). This technique allowed the refinement of chromosomal breakpoints and lead to the identification of seven disrupted genes (GNAQ, RBFOX3, UNC5D, TMEM47, NCAPG2, GTDC1 and XIAP). For one patient we filtered the entire panel of structural variations (SVs) with his parents and identified a unique SV that disrupted a single gene: GTDC1. more...

Organism:: Homo sapiens

Type:: Genome variation profiling by high throughput sequencing

Platforms:: GPL9442 GPL13393
8 Samples

Download data: TXT

Series

Accession:: GSE51430

ID:: 200051430

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20004260819.

Whole-transcriptome high-throughput RNA sequencing of blood leukocytes from Parkinson's disease human patients pre- and post-deep brain stimulation

(Submitter supplied) The given data set is the first deep sequencing transcriptome-wide data set of human Parkinson's disease (PD) patients RNA. The data set was produced from blood leukocytes of PD patients, from the same patients following deep brain stimulation (DBS), and from matched healthy control volunteers. Post-DBS samples were taken from the patients while being on electrical stimulation (ON-Stim), and following one hour off of electrical stimulation (OFF-Stim state). more...