|
| Status |
Public on Jul 11, 2011 |
| Title |
FOXA1 ChIP-seq, 4h DHT treatment |
| Sample type |
SRA |
| |
|
| Source name |
[ChIP] 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: anti-FOXA1
antibody vendor: abcam
antibody catalog#: ab23738
|
| 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 |
FOXA1_MDA-MB-453_4hDHT-ChIP
ChIP-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/)
|
| |
|
| 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 |
SAMN02198504 |
