|
| Status |
Public on May 28, 2015 |
| Title |
Jurkat_CTCF_input |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Jurkat
chip antibody: None
antibody manu.: NULL
antibody catalog: WCE
antibody lot: --
young_id: 20150124_3462
|
| 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 10 min.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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.
Whole cell extracts were sonicated to solubilize the chromatin.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
20150124_3462
|
| Data processing |
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
May 18, 2015 |
| 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) |
| GSE68976 |
Activation of proto-oncogenes by disruption of chromosome neighborhoods [ChIP-Seq] |
| GSE68978 |
Activation of proto-oncogenes by disruption of chromosome neighborhoods |
|
| Relations |
| BioSample |
SAMN03700051 |
| SRA |
SRX1030323 |
