|
| Status |
Public on Jun 04, 2013 |
| Title |
SW620 doxorubicin FAIRE-seq |
| Sample type |
SRA |
| |
|
| Source name |
SW620 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human colon adenocarcinoma
cell line: SW620
treatment: Doxorubicin 20uM
time point: 4 hours post treatment
|
| Treatment protocol |
Tissue culture cells were treated with indicated drugs for 4 hours then fixed and collected for processing. Mice were injected iv with a single dose of the indicated drugs and 4 hours later, tissues were fixed and collected for processing.
|
| Growth protocol |
Tissue culture cells were grown in 15cm dishes around 80% confluency.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FAIRE-seq
|
| Data processing |
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak regions were called by using F-seq package.
|
| |
|
| Submission date |
Nov 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Baoxu Pang |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Michael Snyder
|
| Street address |
3165 Porter Drive
|
| City |
Palo Alto |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE33632 |
Genome-wide analysis of histone eviction by FAIRE-Seq |
| GSE33634 |
Topoisomerase II inhibitors and histone eviction |
|
| Relations |
| SRA |
SRX105585 |
| BioSample |
SAMN00754050 |
