|
| Status |
Public on Apr 15, 2011 |
| Title |
RBC 5d |
| Sample type |
SRA |
| |
|
| Source name |
Red blood cells
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: red blood cell
antibody: CTCF
antibody manufacturer: Millipore
antibody catalog #: 07-729
age: 5 day old
|
| Treatment protocol |
Blood cells were subjected to density gradient centrifugation by Histopaque-1077 (Sigma-Aldrich) to obtain a homogeneous population of mononuclear cells (PBMCs)
|
| Growth protocol |
We cultured PBMCs in RPMI supplemented with 2mM Glutamine, 50 μM Ã-Mercaptoethanol and 10% inactivated fetal bovine serum. Cultured cells were stimulated with 50 ng/ml of PMA and 10 ng/ml Io for 4h at 37oC and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against CTCF
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the chicken (Galgal3) genome using Eland (illumina pipeline). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with SISSRs (http://sissrs.rajajothi.com/).
|
| |
|
| Submission date |
Mar 14, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
David Martin |
| E-mail(s) |
david.martin@crg.es
|
| Phone |
0034 933160169
|
| Organization name |
CRG
|
| Department |
Bioinformatics and Genomics
|
| Lab |
Roderic Guigo
|
| Street address |
C/ Dr. Aiguader, 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL10223 |
| Series (1) |
| GSE27945 |
Genome-wide CTCF binding maps in chicken red blood cells |
|
| Relations |
| BioSample |
SAMN02196881 |
