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Sample GSM648496 Query DataSets for GSM648496
Status Public on Jan 31, 2011
Title aTconv-IgG
Sample type SRA
 
Source name aTconv cells from PBMC, normal
Organism Homo sapiens
Characteristics gender: male
cell type: aTconv cells
chip antibody: IgG
chip antibody vendor: Upstate
Extracted molecule genomic DNA
Extraction protocol the expanded and sorted Treg and aTconv cells were used for ChIP analysis. For mapping enzyme target sites, 2×10e6 cells were crosslinked with formaldehyde and sonicated to obtain chromatin fragments of 200 to 300 bp. Sonicated chromatin was pre-cleared and incubated with 2mg of anti-H3K4me1(Abcam, United Kingdom), anti-H3K3me3 (Abcam) or anti-rabbit IgG (Upstate, USA) overnight at 4°C. The crosslinks were reversed, and The ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced with the Illumina 1G Genome Analyzer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Data processing Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genome using the SOAP(Short Oligonucleotide Analysis Package). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
 
Submission date Jan 04, 2011
Last update date May 15, 2019
Contact name Ni Bing
E-mail(s) nibingxi@yahoo.com
Phone +86-23-68772348
Fax +86-23-68772348
Organization name PLA, Third Military Medical University
Department Institute of Immunology
Street address PLA, Third Military Medical University
City Chongqing
ZIP/Postal code 400038
Country China
 
Platform ID GPL9052
Series (1)
GSE26427 Global Mapping of H3K4me1 and H3K4me3 in human CD4+CD25+FOXP3+ Treg cells
Relations
SRA SRX037434
BioSample SAMN00189625

Supplementary file Size Download File type/resource
GSM648496_IgG.bed.32_MACS_wiggle.tar.gz 4.0 Mb (ftp)(http) TAR
GSM648496_IgG.peak.txt.gz 912.9 Kb (ftp)(http) TXT
GSM648496_IgG.sop.bed.gz 9.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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