|
| Status |
Public on Dec 10, 2010 |
| Title |
HPC control IgG 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-IgG
antibody manufacturer: Santa Cruz Biotechnology
antibody catalog #: sc-66931
|
| 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 IgG
|
| 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) |
[email protected]
|
| 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 |
SRX029316 |
| BioSample |
SAMN00116724 |
