|
| Status |
Public on Oct 23, 2017 |
| Title |
14_A549 RTKi_H3K27Ac [lab: Hammerman-DFCI] |
| Sample type |
SRA |
| |
|
| Source name |
Adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
chip antibody: H3K27Ac
antibody manufacturer: Abcam
antibody catalog number: ab4729-100ug
young_id: 20160603_4858
tissue: Lung
drug: GSK1120212
concentration: 200 nM
cell number: 50 million
treatment duration: 7D
|
| Treatment protocol |
Cells were treated with GSK1120212 (200 nM) for 7 days prior to cross linking with formaldehyde.
|
| Growth protocol |
Cells were grown in RPMI Medium, 10%FBS, 1% penn/strep at 37 degrees and 5% CO2. Cells were maintained between 40-90% confluency.
|
| 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 |
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 24, 2016 |
| 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 (2) |
| GSE89128 |
Suppression of adaptive responses to targeted cancer therapy by transcriptional repression [ChIP-seq] |
| GSE89129 |
Suppression of adaptive responses to targeted cancer therapy by transcriptional repression |
|
| Relations |
| BioSample |
SAMN05938401 |
| SRA |
SRX2267497 |
