|
| Status |
Public on Aug 25, 2012 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 Human Fetal Lung Fibroblast cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
sample type: none
treatment: none
|
| Treatment protocol |
imr90 cells were infected with ER-Ras vector and indicated hairpins. The cells were collected 4 days after tamoxifen treatment. The ChIP experiments were done as previously described (Chicas et al. 2010).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
update
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Input from senescent cells
|
| Data processing |
The immunoprecipitated DNA was prepared for Illumina sequencing as described (Chicas et al. 2010).
The Illumina GA sequencing tags were mapped to the unmasked human reference genome (NCBI version 36, hg18) using the program Bowtie with the parameter setting ‘‘-t -q -a –best –strata -m 1.’’
ChIP-seq peak regions were determined using MACS (Zhang et al. 2008) to find ChIP-enriched regions compared with the input DNA control with default parameter settings and a significance threshold (P<1e-5).
We associated ChIP-enriched regions to a target gene if it localized within the region from 3 kb upstream of to 1 kb downstream from the transcription start site of the gene. The gene coordinates were extracted according to RefSeq gene annotation (hg18) downloaded from the University of California at Santa Cruz Genome Browser.
Genome_build: hg18
|
| |
|
| Submission date |
Aug 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ozlem Aksoy |
| E-mail(s) |
merto@mskcc.org
|
| Phone |
917-930-1718
|
| Organization name |
CSHL
|
| Department |
Watson School of Biological Sciences
|
| Lab |
Scott Lowe's lab
|
| Street address |
415 East 68th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE40343 |
Genome wide maps of E2F7 binding in IMR90 cells |
|
| Relations |
| SRA |
SRX180829 |
| BioSample |
SAMN01129815 |
