|
| Status |
Public on Mar 02, 2015 |
| Title |
Growing IMR90 p53 r1 |
| Sample type |
SRA |
| |
|
| Source name |
diploid fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
factor: p53
condition: Growing
antibody: anti p53 mouse monoclonal (DO-1) Sigma
|
| 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 |
Growing IMR90 anti p53 mouse monoclonal antibody (DO-1) 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.
Principle Component Analysis (PCA) was used to assess the prevalence and quality of read data in TSS regions. Counts were normalized between samples by dividing by effective library size (bin count sums).
The MACS algorithm version 1.4.1 was used together with hg18 aligned, sequence read BAM files for identifying peak regions representing p53 binding sites.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format
|
| |
|
| Submission date |
Dec 19, 2013 |
| 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 |
SAMN02469150 |
| SRA |
SRX396251 |
