|
| Status |
Public on Mar 14, 2012 |
| Title |
LMO1 ChIP-seq Jurkat 2 |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cell line
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: LMO1
antibody catalog number: Santa Cruz SC-10494
antibody manufacturer: Santa Cruz
cell line: Jurkat E6-1
|
| 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 500 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 HiSeq 2000 |
| |
|
| Description |
Chromatin IP against LMO1 ChIP Jurkat
|
| 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) |
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 |
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 |
SRX107307 |
| BioSample |
SAMN00760398 |
