|
| Status |
Public on Nov 13, 2014 |
| Title |
ChIP:H3K27ac_ab4729_Jurkat1_091914 [lab: Look-DFCI] |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Jurkat
chip antibody: H3K27Ac
antibody manu.: Abcam
antibody catalog: ab4729
young_id: 20140924_3101
system: Blood
tal1 enhancer status: WT/Jurkat
|
| Treatment protocol |
Untreated
|
| Growth protocol |
Cells were grown according to ATCC guidelines
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
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 |
Oct 06, 2014 |
| 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 |
GPL16791 |
| Series (1) |
| GSE59657 |
An Oncogenic Super-Enhancer Formed through Somatic Mutation of a Noncoding Intergenic Element |
|
| Relations |
| BioSample |
SAMN03097488 |
| SRA |
SRX725581 |
