|
| Status |
Public on Apr 29, 2013 |
| Title |
BM Scl/Tal1 ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Total bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: bone marrow cells
chip antibody: Scl/Tal1
chip antibody manufacturer: Santa Cruz
chip antibody catalog #: sc-12984
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly isolated bone marrow cells were crosslinked with formaldehyde and sonicated to generate chromatin fragment
Freshly isolated bone marrow cells were crosslinked with formaldehyde and sonicated to generate chromatin fragments, which were immunoprecipitated with Ldb1, Scl/Tal1, Gata1 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 Scl/Tal1
|
| Data processing |
Sequence reads were mapped to the mouse genome (mm8) using the Solexa Analysis Pipeline. The mapped reads for Ldb1, Scl/Tal1, and Gata1 samples were processed using the SISSRs peak-finder (Jothi et al, Nucl Acids Res 2008; PMID: 18684996) with control IgG reads as background and default parameters to identify genome-wide binding sites
Genome_build: mm8
Supplementary_files_format_and_content: BED files containign mapped reads; TEXT files containing the list of binding sites as defined by SISSRS [PMID: 18684996]
|
| |
|
| Submission date |
Dec 11, 2012 |
| 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 |
GPL9185 |
| Series (1) |
| GSE42843 |
Ldb1-nucleated transcription complexes function as primary mediators of erythroid gene activation |
|
| Relations |
| SRA |
SRX209469 |
| BioSample |
SAMN01830692 |
