|
| Status |
Public on May 23, 2012 |
| Title |
RWPE1-ERG ChIP-seq (ERG) |
| Sample type |
SRA |
| |
|
| Source name |
RWPE1-ERG prostate epithelial cell line, ERG ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RWPE1
cell type: benign prostate epithelial cells
overexpressing: truncated ERG
passages: 20
chip antibody: ERG
antibody vendor: Epitomics
antibody catalog #: 2805-1
antibody lot#: YE102106C
|
| Growth protocol |
All cells were grown in medium following ATCC recommended conditions. Briefly, the base medium for this cell line is provided by Invitrogen (GIBCO) as part of a kit: Keratinocyte Serum Free Medium (K-SFM), Kit Catalog Number 17005-042. This kit is supplied with each of the two additives required to grow this cell line (bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF) at the following concentrations: 0.05 mg/ml BPE - provided with the K-SFM kit. 5 ng/ml EGF - provided with the K-SFM kit.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using phenol/chloroform and Qiagen MinElute extraction. All library constructions were generated following recommended protocols and reagents from Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RWPE1 cell line stably over-expressing truncated ERG encoded by the most common TMPRSS2-ERG isoform.
|
| Data processing |
ChIP-seq: Base-calling was done using the standard Illumina pipeline. We aligned the ChIP-seq reads to the hg18 human genome using BWA and identified ERG-binding sites using ChIPseeqer.
Genome_build: hg18
Supplementary_files_format_and_content: ChIPseeqer: Each row corresponds to a peak. For details, please go to: http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_use
Processed data files are linked to the Series record as supplementary files.
|
| |
|
| Submission date |
May 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Soong |
| Organization name |
Weill Cornell Medical College
|
| Department |
Institute for Computational Biomedicine
|
| Street address |
1305 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE37752 |
Oncogene-Mediated Alterations in Chromatin Conformation |
|
| Relations |
| SRA |
SRX145843 |
| BioSample |
SAMN00990802 |
