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Series GSE120738 Query DataSets for GSE120738
Status Public on Oct 03, 2018
Title Integrative epigenetic taxonomy of primary prostate cancer [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Androgen Receptor (AR) is the key-driving transcription factor in prostate cancer, tightly controlled by epigenetic regulation. To date, most epigenetic profiling has been performed in cell lines or limited tissue samples. To comprehensively study the epigenetic landscape, we complemented RNA-seq with ChIP-seq for AR and histone modification marks (H3K27ac, H3K4me3, H3K27me3) in 100 primary prostate carcinomas. Integrative molecular subtyping of the five data streams revealed three major subtypes of which two were clearly TMPRSS2-ERG dictated. Importantly, a third novel subtype was identified, with low AR chromatin binding and activity, even though the receptor was clearly expressed. While positive for neuroendocrine-hallmark genes, these tumors were copy number-neutral with low mutation burden, significantly depleted for genes characteristic of poor-outcome associated luminal B-subtype. We present a rich novel resource on transcriptional and epigenetic control in prostate cancer, revealing a tight control of gene regulation differentially dictated by AR over the three subtypes.
Overall design AR, H3K27ac, H3K4me3 and H3K27me3 ChIP-seq data for primary prostate carcinomas
Contributor(s) Zwart W, Stelloo S, Kim Y, Nevedomskaya E
Citation(s) 30464211
Submission date Oct 02, 2018
Last update date Mar 27, 2019
Contact name Suzan Stelloo
Organization name Radboud University
Department Molecular Biology
Street address Geert Grooteplein Zuid 28
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (312)
GSM3409642 P223T_AR
GSM3409643 P227T_AR
GSM3409644 P228T_AR
This SubSeries is part of SuperSeries:
GSE120742 Integrative epigenetic taxonomy of primary prostate cancer
BioProject PRJNA494344
SRA SRP163171

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE120738_RAW.tar 70.7 Mb (http)(custom) TAR (of BED, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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