 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 26, 2011 |
| Title |
Th17-Gata3 [ChIP-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
T-helper 17 cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: T-helper 17 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 |
|
| Relations |
| SRA |
SRX018108 |
| BioSample |
SAMN00010537 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM523228_GA1715_mm8_Th17_GATA3.bed.gz |
23.1 Mb |
(ftp)(http) |
BED |
| GSM523228_Th17-GATA3.bsites.bedgraph.gz |
3.5 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
