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Series GSE43720 Query DataSets for GSE43720
Status Public on Jan 01, 2015
Title Redefinition of Human Androgen Responsive Elements [MNase-Seq, ChIP_seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The androgen receptor (AR) mediates the action of androgens by binding to androgen-responsive elements (AREs) and subsequently regulating target genes involved in prostate carcinogenesis. The precise locations, true nature, and functional roles of AREs in human prostate cancer are still unknown. Here we redefine AREs by motif-resolution AR chromatin immunoprecipitation-exonuclease (ChIP-exo) assay in human prostate cancer cells and tumors. Surprisingly, we find that, in addition to canonical full-length AREs and half-site-like AREs, a significant portion of the four redefined ARE categories comprises non-canonical full-length AREs. The redefined AREs in enhanced AR binding regions in prostate tumors versus paired non-malignant adjacent tissues regulate a prostate cancer-relevant gene network not only centered on AR, but more interestingly, on novel AR target genes mTOR, BIRC5 and BCL2L1 involved in prostate cancer cell growth and survival. The precise redefinition of AREs has important implications for understanding how AR contributes to prostate carcinogenesis.
Overall design To examine the differential AR binding in LNCaP cells before and after androgen stimulation, ChIP-Seq of androgen receptor is performed in LNCaP cells under the two conditions. To profile histone modification status in control LNCaP cells, MNase-Seq is performed with five different antibodies specific to certain histone marks. Each experiment includes two replicates.
Contributor(s) Wang Q, Chen Z
Citation(s) 25535248
Submission date Jan 24, 2013
Last update date May 15, 2019
Contact name Xun Lan
Phone 7738345917
Organization name Stanford University
Department Genetics
Lab Pritchard's Lab
Street address 318 Campus Dr. Room S240
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (14)
GSM1069669 LNCaP_CON_rep1
GSM1069670 LNCaP_CON_rep2
GSM1069671 H3K27Me3_rep1
This SubSeries is part of SuperSeries:
GSE43791 Redefinition of Human Androgen Responsive Elements
BioProject PRJNA187481
SRA SRP018231

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE43720_RAW.tar 1.9 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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