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Sample GSM359413 Query DataSets for GSM359413
Status Public on Jan 20, 2009
Title E14Tg2a murine ES cells Brg J1
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
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
SRA SRX003888
BioSample SAMN02195575

Supplementary file Size Download File type/resource
GSM359413_mm8-EScell-Brg-J1B-binding-regions.txt.gz 95.5 Kb (ftp)(http) TXT
GSM359413_mm8-EScell-Brg-J1B.bed.gz 106.7 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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