|
| Status |
Public on Jun 30, 2010 |
| Title |
ER_DBDmut-ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MDA-MB 231 cells stably expressing ER
genotype/variation: DBDmut-ER
antibody: ERa
antibody manufacturer: HC20 Santa Cruz
cell amount: 20 million Cells
|
| Treatment protocol |
Cells were treated with 10 nM E2 for 45 minutes, fixed with 1% formaldehyde for 10 minutes and sonicated to shear chromatin.
|
| Growth protocol |
Cells were grown in phenol-red free DMEM-Ham's F-12 media with 10 mM HEPES, 10% Charcoal-dextran stripped media, 6 ng/ml bovine insulin, 3.75 ng/ml Hydrocortisone and 16 ug/ml glutathione.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sonicated and precipitated using an specific antibody for ERa (HC20,Santa Cruz)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against Estrogen Receptor
|
| Data processing |
Alignment: Reads were truncated to 25 bp and aligned to the human hg18 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Peak Identification: Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/). Peaks were found by identifying 200 bp regions with tag density exceeding a threshold set at a 0.1% false discovery rate (determined by tag randomization). Only peaks with >4x normalized tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region were considered for analysis
|
| |
|
| Submission date |
Jun 29, 2010 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Joshua D Stender |
| Organization name |
University of California at San Diego
|
| Street address |
9500 Gillman
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE22609 |
Genome-Wide Maps of WT and DBDmut Estrogen Receptor in Human Breast Cancer Cells |
| GSE22610 |
Genome-Wide Analysis of Estrogen Receptor-α DNA Binding and Tethering Mechanisms |
|
| Relations |
| BioSample |
SAMN02196073 |
