|
| Status |
Public on Jan 01, 2015 |
| Title |
Redefinition of Human Androgen Responsive Elements [ChIP-Seq, RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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.
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| |
|
| Overall design |
To accurately define ARE in human genome and identify cancer related AR binding site, AR ChIP-exo is performed in LNCaP cells before/after androgen stimulation, malignant prostate tumors and non-malignant adjacent tissues. Each experiment includes two replicates.
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| |
|
| Contributor(s) |
Wang Q, Chen Z |
| Citation(s) |
25535248 |
| Submission date |
Jan 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xun Lan |
| E-mail(s) |
xlan@stanford.edu
|
| 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) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (20)
|
| GSM1071279 |
LNCaP control [RNA-seq replicate 2 ] |
| GSM1071280 |
LNCaP DHT treated [ChIP-exo replicate 1 ] |
| GSM1071281 |
LNCaP DHT treated [ChIP-exo replicate 2 ] |
| GSM1071282 |
LNCaP DHT treated [RNA-seq replicate 1 ] |
| GSM1071283 |
LNCaP DHT treated [RNA-seq replicate 2 ] |
| GSM1071284 |
non-malignant adjacent tissue 1 (N1) [ChIP-exo replicate 1 ] |
| GSM1071285 |
non-malignant adjacent tissue 1 (N1) [ChIP-exo replicate 2 ] |
| GSM1071286 |
non-malignant adjacent tissue 2 (N2) [ChIP-exo replicate 1 ] |
| GSM1071287 |
non-malignant adjacent tissue 2 (N2) [ChIP-exo replicate 2 ] |
| GSM1071288 |
malignant prostate tumor 1 (M1) [ChIP-exo replicate 1 ] |
| GSM1071289 |
malignant prostate tumor 1 (M1) [ChIP-exo replicate 2 ] |
| GSM1071290 |
malignant prostate tumor 2 (M2) [ChIP-exo replicate 1 ] |
| GSM1071291 |
malignant prostate tumor 2 (M2) [ChIP-exo replicate 2 ] |
| GSM1071292 |
malignant prostate tumor 3 (M3) [ChIP-exo replicate 1 ] |
| GSM1071293 |
malignant prostate tumor 3 (M3) [ChIP-exo replicate 2 ] |
| GSM1071294 |
malignant prostate tumor 4 (M4) [ChIP-exo replicate 1 ] |
| GSM1071295 |
malignant prostate tumor 4 (M4) [ChIP-exo replicate 2 ] |
|
| This SubSeries is part of SuperSeries: |
| GSE43791 |
Redefinition of Human Androgen Responsive Elements |
|
| Relations |
| BioProject |
PRJNA187482 |
| SRA |
SRP018241 |
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