|
| Status |
Public on May 04, 2016 |
| Title |
p53-KO |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 colon cancer cells, p53-KO, p53 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colon cancer cell line
genotype/variation: p53-KO
treatment: DMSO
chip antibody: p53
|
| Treatment protocol |
ATF3-wildtype (ATF3-WT), -knockout (ATF3-KO), p53-knockout (p53-KO) cells were treated with DMSO (Ctrl) or 1.5 uM of camptothecin (CPT) for 4 h, and then crosslinked by 1 mM of di(N-succinimidyl) glutarate (DSG) for 45 min and 1% of formaldehyde for 10 min.
|
| Growth protocol |
Cells were generated by AAV-mediated homologous recombination.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared by sonication using Bioruptor to an average fragment size of 500 bp, immunoprecipitated using the indicated antibody, purified and sequenced using Illumina HiScanSQ following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Chromatin IP against p53.
|
| Data processing |
Reads were aligned to the hg19 reference human genome using bwa v0.6.1.
Peak-calling by HOMER v4.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph files, HOMER peak output files.
|
| |
|
| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan.yu@emory.edu
|
| Organization name |
Emory University
|
| Department |
Urology
|
| Lab |
Jindan Yu's lab
|
| Street address |
E330, 1760 Haygood Dr NE
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE74355 |
The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation [ChIP-seq] |
| GSE74363 |
The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation |
|
| Relations |
| BioSample |
SAMN04216078 |
| SRA |
SRX1384028 |
