|
| Status |
Public on Sep 14, 2017 |
| Title |
Doxorubicin-treated ATRX ChIP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Dedifferentiated liposarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LS8817
drug treatment: Doxorubicin
|
| Treatment protocol |
Cells were treated 1μM PD0332991, 100nM doxorubicin or cultured in DME-HG media containing only 0.5% serum for 7 days. Media was changed and drugs were replenished after 3 days.
|
| Growth protocol |
LS8817 cells were grown in DME-HG supplemented with 10% FBS (unless otherwise indicated) and split as necssary, usually 1:3 every 3 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with ATRX antibody using magnetic beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DDLS-doxo_ATRX_rep1
|
| Data processing |
FASTQ files were adapter and quality trimmed using Trim Galore! v0.3.3
Reads were aligned to hg19 using BWA (mem) v0.7..8
Aligned reads were indel realigned and base quality recalibrated using GATK v3.1.1
Peaks were called using MACS v2.0.10
False positive peaks were reduced using IDR in phantompeakqualtools v1.1
Genome_build: hg19
Supplementary_files_format_and_content: bigWig signal files normalized by total reads, broadPeak calls, and IDR optimal peak calls
|
| |
|
| Submission date |
Nov 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Koff |
| E-mail(s) |
a-koff@ski.mskcc.org
|
| Organization name |
Sloan Kettering Institute
|
| Department |
Molecular Biology
|
| Lab |
Cell Cycle Regulation
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE74619 |
ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence [ChIP-Seq] |
| GSE74621 |
ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence |
|
| Relations |
| BioSample |
SAMN04231487 |
| SRA |
SRX1410755 |
