|
| Status |
Public on Jan 20, 2009 |
| Title |
E14Tg2a murine ES cells IgG |
| Sample type |
SRA |
| |
|
| Source name |
E14Tg2a murine ES cells
|
| Organism |
Mus musculus |
| Characteristics |
ES cells
|
| Treatment protocol |
Cells were grown under standard conditions and were not subjected to further treatment before harvesting for ChIP-Seq experiments
|
| Growth protocol |
E14 ES cells were cultured in Knockout Dulbecco’s modified eagle medium (Gibco, Cat# 10829) supplemented with 15% ES-qualified FBS (Invitrogen, Cat#16141-079), 2mM L-glutamine (Gibco #25030-081), 10mM HEPES (Gibco #15630-080), 100U/ml penicillin/streptomycin (Gibco #15070-063), 0.1mM non-essential amino acids (Gibco #11140-050), 0.1mM beta-mercaptoethanol (Gibco #21985-023) and 1000U/ml LIF (Esgro, Chemicon #ESG1107). ES cells were maintained at 37°C, 7% carbon dioxide, fed with fresh media daily, and passaged onto new plates following trypsin dissociation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For chromatin immunoprecipitation (ChIP) using a anti-Brg/Brm antibody (Clone J1, Khavari et al., 1993, Nature, PMID: 8232556), the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200-500 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
n/a
|
| Data processing |
Sequenced 25-bp reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. Reads that mapped to unique genomic locations with at most 2 mismatches were processed further to using the TIROE algorithm to identify genomic regions enriched with mapped reads with p-value threshold E-10.
|
| |
|
| Submission date |
Jan 12, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Raja Jothi |
| E-mail(s) |
jothi@mail.nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Environmental Health Sciences
|
| Lab |
Systems Biology
|
| Street address |
111 TW Alexander Drive; A314
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE14344 |
esBAF is an essential component of the core pluripotency transcriptional network |
|
| Relations |
| SRA |
SRX003889 |
| BioSample |
SAMN02195576 |
