|
| Status |
Public on Oct 31, 2015 |
| Title |
Checkpoint IMR90 H3K36me3 |
| Sample type |
SRA |
| |
|
| Source name |
human diploid fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: human diploid fibroblast
treated with: Etoposide for 24hrs
histone marks to be tested: K36me3
condition: DDR; acute DNA damage response (24 hour Etoposide treated)
chip antibody: mouse monoclonal H3K36me3 antibody, clone CMA333 (PMID: 20824077)
|
| Treatment protocol |
24 hours Etoposide (100microM),pBabe-Puro H-RasG12V, pWXL-Hygro E2A, H-RasG12V, pLNCX-Neo ER:H-RasG12V overexpression
|
| Growth protocol |
cultured in 5%O2 in DMEM with 10% FBS and Pen/Strep and Glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina Genome Analyzer according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
24 hour Etoposide treated IMR90 anti Histone H3K36me3 CMA333 ChIP Seq
|
| Data processing |
Single-end reads were aligned against the Human Reference Genome (assembly hg18, NCBI Build 36) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Genome_build: hg18
Supplementary_files_format_and_content: tdf (converted from wig files) containing data that has been preprocessed for faster display in IGV
|
| |
|
| Submission date |
Oct 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chandra Chilamakuri |
| E-mail(s) |
datasubmissions@cruk.cam.ac.uk
|
| Organization name |
Cancer Research UK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE53491 |
Phenotype specific analyses of p53 reveal distinct regulatory mechanism for chronically activated p53 |
|
| Relations |
| BioSample |
SAMN04226994 |
| SRA |
SRX1403826 |
