|
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 |
E-mail(s) |
jothi@mail.nih.gov
|
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. |
|
Relations |
SRA |
SRX029315 |
BioSample |
SAMN00116723 |