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Series GSE25183 Query DataSets for GSE25183
Status Public on Aug 02, 2011
Title Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression (RNA-Seq data)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.
 
Overall design 21 prostate cell lines sequenced on the Illumina Genome Analyzer and GAII. Variable number of replicates per sample. RNA-Seq data from prostate cancer tissues used in this study will be made available on dbGAP.
 
Contributor(s) Chinnaiyan AM, Iyer M, Prensner J
Citation(s) 21804560
Submission date Nov 08, 2010
Last update date Feb 21, 2019
Contact name Matthew Iyer
E-mail mkiyer@med.umich.edu
Phone 7346154503
Organization name University of Michigan
Department Michigan Center for Translational Pathology
Lab Chinnaiyan Lab
Street address 5316 CCGC 0940 1400 E. Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48109-0940
Country USA
 
Platforms (2)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (58)
GSM618463 22Rv1_sr_rep1
GSM618464 22Rv1_pe_rep1
GSM618465 C4-2B_pe_rep1
This SubSeries is part of SuperSeries:
GSE31728 Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
Relations
SRA SRP004637
BioProject PRJNA153913

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25183_RAW.tar 16.3 Gb (http)(custom) TAR (of BAM)
Raw data are available in SRA
Processed data provided as supplementary file

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