|
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 |