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Status |
Public on Jul 11, 2011 |
Title |
AR 4h input-seq, 4h DHT treatment |
Sample type |
SRA |
|
|
Source name |
[input] MDA-MB-453 cells treated with 10nM DHT for 4h
|
Organism |
Homo sapiens |
Characteristics |
cell line: MDA-MB-453 breast cancer cell line agent: DHT time: 4hr antibody: none (input control)
|
Treatment protocol |
The MDA-MB-453 cells were grown in the phenol red-free medium supplemented with 5% charcoal/dextran-treated fetal bovine serum for 3 days, followed by treatment of 10 nM DHT for 4h and 16h respectively for ChIP after crosslinking with 1% formadehyde.
|
Growth protocol |
The MDA-MB-453 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37C incubator.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
6 ng ChIP DNA was used in the direct polyA tailing step according to Helicos HeliScope standard procedure.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Helicos HeliScope |
|
|
Description |
AR_MDA-MB-453_4hDHT-Input Input-seq data sequencing instrument: HeliScope Single Molecule Sequencer
|
Data processing |
Aligment: Sequence reads were obtained and mapped the human genome (hg18, March 2006) using Helicos Genetic Analysis System. Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm, version 1.3.7.1 (http://liulab.dfci.harvard.edu/MACS/)
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|
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Submission date |
Apr 21, 2011 |
Last update date |
Jun 11, 2013 |
Contact name |
Yiwen Chen |
E-mail(s) |
ychen26@mdanderson.org
|
Organization name |
University of Texas MD Anderson Cancer Center
|
Department |
Bioinformatics and Computational Biology
|
Lab |
Yiwen Chen
|
Street address |
1400 Pressler Street
|
City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL14761 |
Series (2) |
GSE28788 |
Androgen receptor cistrome in breast cancer cell line MDA-MB-453 with 5a-dihydrotestosterone (DHT) stimulation |
GSE28789 |
Breast cancer cell line MDA-MB-453 response to DHT |
|
Relations |
BioSample |
SAMN02198506 |