|
| Status |
Public on Nov 30, 2010 |
| Title |
IgG |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ T cells, control ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ T cells
antibody: normal rabbit IgG
antibody vendor: Santa Cruz
antibody catalog #: SC-2027
|
| Growth protocol |
Human CD4+ T cells were isolated as described in Barski et al., Cell 2007 (PMID 17512414).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Prior to ChIP experiments, cells were cross-linked with formaldehyde and sonicated to obtain DNA fragments ranging in size from 150-200bp. Library preparation was performed as described in Barski et al., Cell 2007 (PMID 17512414).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Control for IP with IgG antibody.
|
| Data processing |
Sequence reads were obtained and mapped to the human hg18 (NCBI Build 36; March 2006) genome using the Illumina Genome Analyzer Pipeline. All reads aligning with two or fewer mismatches were retained for further analysis. Peak detection was performed with the SICER algorithm (http://home.gwu.edu/~wpeng/Software.htm).
|
| |
|
| Submission date |
Nov 29, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
dschones@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE25674 |
Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions |
|
| Relations |
| SRA |
SRX032597 |
| BioSample |
SAMN00139428 |
| Named Annotation |
GSM630811_IgG.aligned.bed.gz |
