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| Status |
Public on Aug 26, 2011 |
| Title |
DN-Gata3 [ChIP-Seq] |
| Sample type |
SRA |
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| Source name |
Double negative cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Double negative cells
chip antibody: anti-Gata3 (558686, BD bioscience)
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| Treatment protocol |
n/a
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Gata3 ChIP-Seq
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| 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.
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| Submission date |
Mar 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian J Abraham |
| Organization name |
St. Jude Children's Research Hospital
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| Department |
Computational Biology
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| Street address |
262 Danny Thomas Blvd
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38112 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE20898 |
Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types |
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| Relations |
| 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 Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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