|
| Status |
Public on May 18, 2010 |
| Title |
VCaP_R1881_AR_jy12 |
| Sample type |
SRA |
| |
|
| Source name |
VCaP - R1881 - Chromatin IP against AR
|
| Organism |
Homo sapiens |
| Characteristics |
R1881
|
| Growth protocol |
Prostate cell lines were maintained in appropriate medium. For androgen treatment experiment, LNCaP and VCaP cells were hormone starved for 48 hours prior to treatment with ethanol control or synthetic androgen R1881. For RNA interference of ERG, VCaP cells were grown in regular medium and subjected to non-silencing control siRNA or siRNA specific for targeting ERG on two continuous days. At 48 hour after the last siRNA transfection, cells were harvested for ChIP analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against AR
|
| Data processing |
Reads were aligned to the reference genome using Eland software (Illumina). Enriched intervals were identified by a Hidden Markov Model-based program named HPeak (Qin et al. unpublished).
|
| |
|
| Submission date |
Dec 22, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan-yu@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Medicine - Hem/Onc
|
| Lab |
Yu
|
| Street address |
303 E. Superior St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE14092 |
An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression (II) |
| GSE14097 |
An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression |
|
| Relations |
| SRA |
SRX022572 |
| BioSample |
SAMN00016585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM353646_JY-12_1_eland_result.txt.gz |
143.2 Mb |
(ftp)(http) |
TXT |
| GSM353646_JY-12_2_eland_result.txt.gz |
141.6 Mb |
(ftp)(http) |
TXT |
| GSM353646_JY-12_3_eland_result.txt.gz |
143.1 Mb |
(ftp)(http) |
TXT |
| GSM353646_jy12s678VCAR.allregions.txt.gz |
263.3 Kb |
(ftp)(http) |
TXT |
| GSM353646_s_1_export.txt.gz |
101.7 Mb |
(ftp)(http) |
TXT |
| GSM353646_s_2_export.txt.gz |
202.1 Mb |
(ftp)(http) |
TXT |
| GSM353646_s_6_export.txt.gz |
46.0 Mb |
(ftp)(http) |
TXT |
| GSM353646_s_7_export.txt.gz |
95.0 Mb |
(ftp)(http) |
TXT |
| GSM353646_s_8_export.txt.gz |
181.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
