|
| Status |
Public on Oct 01, 2015 |
| Title |
LNCaP-AR_Vehicle_AR_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-AR
cell type: Prostate cancer
chip antibody: AR (Millipore, 06-680)
|
| Treatment protocol |
LNCaP-AR cells were grown in charcoal-stripped serum containing phenol-red free media for 72hrs and then treated with vehicle or 1nM R1881 or 1nM R1881 plus 10µM Bicalutamide or 1nM R1881 plus 10µM MDV3100 for 1hr. VCaP and CWR22PC cells were grown in regular media and treated with vehicle or 1nM DHT or 1nM DHT plus 10µM Bicalutamide or 1nM DHT plus 10µM MDV3100 for 1hr.
|
| Growth protocol |
LNCaP-AR cells were grown in RPMI containing 10% FBS, VCaP cells were grown in DMEM containing 10% FBS, CWR22PC cells were grown in RPMI containing 10% FBS plus 0.1nM DHT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP library was prepared for sequencing by the SOLiD (LNCaP-AR and VCaP) or HiSeq2000 (CWR22PC) instruments according to manufacturer recommended procedures.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
Chromatin IP against AR
|
| Data processing |
Alignment: ChIP-seq reads were obtained and mapped to the human genome (hg18, build 36) using either the AB SOLiD pipeline (LNCaP-AR and VCaP) or the Illumina CASAVA pipeline (v1.8.0; CWR22PC). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification and data analysis.
Peak detection was performed with the software MACS (Version 1.4.0) with input as controls.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data are peaks in the standard bed format.
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Chen
|
| Street address |
1275 York Ave, Box 20
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9442 |
| Series (2) |
| GSE62442 |
Androgen receptor DNA binding in response to different ligands across three prostate cancer cell lines |
| GSE62472 |
Cell context specific effect of AR antagonists on AR DNA binding and target gene expression |
|
| Relations |
| BioSample |
SAMN03113126 |
| SRA |
SRX734399 |
