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Sample GSM523221 Query DataSets for GSM523221
Status Public on Aug 26, 2011
Title DN-Gata3 [ChIP-Seq]
Sample type SRA
Source name Double negative cells
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Double negative cells
chip antibody: anti-Gata3 (558686, BD bioscience)
Treatment protocol n/a
Growth protocol DN, DP, Naive CD4, nTreg and NKT cells are directly separated from mice. CD8, Th1, Th2, Th17 and iTreg cells are cultured in specifc growth media.
Extracted molecule genomic DNA
Extraction protocol Following standard ChIP-seq protocol. Chromatin from 1 × 107 cells was used for each ChIP experiment, which yielded approximately 100 ng of DNA. Antibodies against GATA3 (558686, BD bioscience) was used. After reverse cross-linking and purification with Qiagen PCR purification kit, the ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced using the Illumina 1G Genome Analyzer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
Description Gata3 ChIP-Seq
Data processing Reads were aligned against genome build mm8 using ELAND. .bsites (bedgraph) files were created using MACS (Model-based Analysis for ChIP-Seq) version 1.4.0, with a p-value threshold of 1e-13 and no redundant reads used.
Submission date Mar 16, 2010
Last update date May 15, 2019
Contact name Brian J Abraham
Organization name St. Jude Children's Research Hospital
Department Computational Biology
Street address 262 Danny Thomas Blvd
City Memphis
State/province TN
ZIP/Postal code 38112
Country USA
Platform ID GPL9250
Series (1)
GSE20898 Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types
SRA SRX018101
BioSample SAMN00010530

Supplementary file Size Download File type/resource
GSM523221_DN-GATA3.bsites.bedgraph.gz 36.9 Kb (ftp)(http) BEDGRAPH
GSM523221_DN-Gata3.bed.gz 84.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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