|
| Status |
Public on Oct 23, 2014 |
| Title |
H82 input |
| Sample type |
SRA |
| |
|
| Source name |
Small Cell Lung Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NCI-H82
chip antibody: None
young_id: 20140124_3120
system: Lung
cell number: 20 million
drug: DMSO
concentration: 0.1%
time point: 6 hrs
|
| Treatment protocol |
Cells were grown at 0.5x10^6 cells in RPMI medium and treated with DMSO for 6 hours and then cross linked with formaldehyde.
|
| Growth protocol |
NCI-H82 cells were obtained from ATCC and grown in RPMI with 10% FBS and 1% penn/strep. NCI-H82 cells were grown and passaged at 0.5x10^6 cells /ml.
|
| 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 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 in 50 bp bins with each read extended 200 in the direction of alignment as calculated by MACS and normalized to million mapped reads
Supplementary_files_format_and_content: Corrected WIG files represent counts of aligned reads in 50 bp bins with each read extended 200bp in the direction of alignment as calculated by MACS. Background correction was used by subtracting values from the Input RPM-normalized WIG from the H3K27ac RPM-normalized WIG
|
| |
|
| Submission date |
Oct 16, 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 (2) |
| GSE62412 |
Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor (ChIP-seq) |
| GSE62614 |
Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor |
|
| Relations |
| BioSample |
SAMN03112916 |
| SRA |
SRX734237 |
