|
| Status |
Public on Oct 20, 2008 |
| Title |
CD4+ T cell CTCF |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells
|
| Organism |
Homo sapiens |
| Characteristics |
primary T cell
antibody: CTCF cell type: CD4+ T cells
|
| Growth protocol |
CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi). Hela cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1 mM glutamine. Jurkat cells were maintained in RPMI supplemented with 10% fetal bovine serum and 1 mM glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For chromatin immunoprecipitation (ChIP) using a CTCF antibody (upstate 07-729), the formaldehyde cross-linked cells were sonicated to obtain DNA fragments ranging in size from ~200 bp. Cluster generation and sequencing were performed as described earlier (Barski et al Cell, 2007) . MNase digested, mononucleosome sized DNA fragments were used for H3K27me3 and H2AK5ac ChIPs .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against CTCF
|
| Data processing |
Sequence reads were mapped to the human genome (hg18) using the Solexa Analysis Pipeline. The mapped CTCF reads were processed using the SISSRs algorithm (Jothi et al, Nucl Acids Res 2008) to identify genome-wide binding sites locations. The mapped H3K27me3 reads were first grouped into 1000 bp summary windows, following which “islands” of summary windows enriched with H3K27me3 tags were identified as domains using an approach similar to that used in our earlier study (Barski et al, Cell 2007). A CTCF binding site, denoted by genomic coordinate x, is defined as a barrier site relative to an H3K27me3 domain d of length l, only if the distance between x and the domain boundary is at most the smaller of l/10 and 1000 bp.
|
| |
|
| Submission date |
Oct 01, 2008 |
| 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) |
| GSE12889 |
CTCF demarcates chromatin domains |
|
| Relations |
| SRA |
SRX003794 |
| BioSample |
SAMN02195711 |
