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Sample GSM630809 Query DataSets for GSM630809
Status Public on Nov 30, 2010
Title HMGN1
Sample type SRA
 
Source name CD4+ T cells, HMGN1 ChIP
Organism Homo sapiens
Characteristics cell type: CD4+ T cells
antibody: rabbit anti-HMGN1
Growth protocol Human CD4+ T cells were isolated as described in Barski et al., Cell 2007 (PMID 17512414).
Extracted molecule genomic DNA
Extraction protocol Prior to ChIP experiments, cells were cross-linked with formaldehyde and sonicated to obtain DNA fragments ranging in size from 150-200bp. Library preparation was performed as described in Barski et al., Cell 2007 (PMID 17512414).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Chromatin IP against HMGN1.
Antibody to purified HMGN1 (Bustin et al. (1978) J. Bio. Chem. 253, 1694 (PMID 75209)) were prepared in rabbits and affinity purified on HMGN1-containing sepharose as described in Bustin (1989) Methods in Enzymol. 170, 214 (PMID 2770539).
Data processing Sequence reads were obtained and mapped to the human hg18 (NCBI Build 36; March 2006) genome using the Illumina Genome Analyzer Pipeline. All reads aligning with two or fewer mismatches were retained for further analysis. Peak detection was performed with the SICER algorithm (http://home.gwu.edu/~wpeng/Software.htm).
 
Submission date Nov 29, 2010
Last update date May 15, 2019
Contact name Dustin E Schones
E-mail(s) dschones@coh.org
Organization name City of Hope
Street address 1500 E Duarte Rd.
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL10999
Series (1)
GSE25674 Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions
Relations
SRA SRX032595
BioSample SAMN00139426
Named Annotation GSM630809_HMGN1.aligned.bed.gz
Named Annotation GSM630809_HMGN1.peaks.bed.gz

Supplementary file Size Download File type/resource
GSM630809_HMGN1.aligned.bed.gz 166.7 Mb (ftp)(http) BED
GSM630809_HMGN1.peaks.bed.gz 1.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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