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Sample GSM612960 Query DataSets for GSM612960
Status Public on Dec 10, 2010
Title HPC GABPa ChIP-Seq
Sample type SRA
Source name CD34+CD133+ hematopoietic progenitor cells (HPCs)
Organism Homo sapiens
Characteristics cell type: CD34+CD133+ hematopoietic progenitor cells (HPCs)
antibody: anti-GABP-alpha
antibody manufacturer: Santa Cruz Biotechnology
antibody catalog #: sc-22810
Growth protocol CD34+CD133+ HPCs were isolated from healthy blood donors.
Extracted molecule genomic DNA
Extraction protocol Freshly isolated HPCs were crosslinked with formaldehyde and sonicated to generate chromatin fragments, which were immunoprecipitated with GABP-alpha or control IgG antibody. The DNA fragments were end-repaired and processed for sequencing on an Illumina Genome Analyzer using standard protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Chromatin IP against GABP-alpha
Data processing Sequence reads were mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The mapped GABP-alpha reads were processed using the SISSRs peak-finder (Jothi et al, Nucl Acids Res 2008; PMID: 18684996) with control IgG reads as background to identify genome-wide GABP-alpha binding sites.
Submission date Oct 26, 2010
Last update date May 15, 2019
Contact name Raja Jothi
Organization name National Institutes of Health
Department National Institute of Environmental Health Sciences
Lab Systems Biology
Street address 111 TW Alexander Drive; A314
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL9052
Series (1)
GSE24933 Genome-wide mapping of the transcription factor GABP-alpha binding in human CD34+CD133+ hematopoietic progenitor cells.
SRA SRX029315
BioSample SAMN00116723

Supplementary file Size Download File type/resource
GSM612960_hg18-CD34-GABPa-control-e10p01.bsites.txt.gz 142.2 Kb (ftp)(http) TXT
GSM612960_hg18-CD34-GABPa.bed.gz 37.4 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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