|
| Status |
Public on Mar 14, 2012 |
| Title |
E2A ChIP-seq CCRF-CEM |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: TCF3/E2A
antibody catalog number: Santa Cruz SC-349
antibody manufacturer: Santa Cruz
cell line: CCRF-CEM
|
| Growth protocol |
Human CCRF-CEM cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against E2A ChIP CEM
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
hg18
|
| |
|
| Submission date |
Nov 21, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
[email protected]
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE29181 |
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia |
| GSE33850 |
Core transcriptional regulatory circuit controlled by the tal1 complex in human t-cell acute lymphoblastic leukemia (Subseries) |
|
| Relations |
| SRA |
SRX107286 |
| BioSample |
SAMN00760377 |
