|
| Status |
Public on Feb 09, 2012 |
| Title |
TCF3/E2A ChIP-seq in Jurkat |
| Sample type |
SRA |
| |
|
| Source name |
10162009_42YHYAAXX_B2
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: TCF3/E2A
antibody catalog number: Santa Cruz SC-349X
cell line: Jurkat E6-1
cell number: 30 million
|
| Growth protocol |
Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. 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 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against E2A Jurkat
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to the hg18 build using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5 reads per million are shown.
|
| |
|
| Submission date |
May 10, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| 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 |
GPL9115 |
| Series (2) |
| GSE29180 |
ChIP-Seq of TAL1 and its regulatory partners in T-ALL cells |
| GSE29181 |
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia |
|
| Relations |
| SRA |
SRX128780 |
| BioSample |
SAMN00811034 |
