|
| Status |
Public on Jul 01, 2013 |
| Title |
U2OS_Nutlin_p53chip |
| Sample type |
SRA |
| |
|
| Source name |
U2OS cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: U2OS
cell type: osteosarcoma
treatment: 10 uM Nutlin-3 for 24 hr and ChIP with p53
chip antibody: p53 DO-1 (Santa Cruz, sc-126)
|
| Treatment protocol |
for No Treatment: none; Doxorubicin: 0.6 ug/ml Doxorubicin for 24 hrs; DMSO; 0.1% DMSO for 24 hrs; Nutlin: 10 uM Nutlin-3 for 24 hrs
|
| Growth protocol |
U2OS expressing endogenous wild-type p53 was maintained in McCoy's 5A medium supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin at 37ºC in 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Treated cells were crosslinked with 1% formaldehyde then cells were lysed and nuclei were collected. Chromatin was sheared and immunoprecipitated with p53 DO-1 Ab overnight. Input DNA and p53 ChIP-DNA were reverse crosslinked and purified.
Libraries were prepared the using the Illumina ChIP-seq DNA Sample Prep Kit as per manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
U2OS cells treated with 10 uM Nutlin-3 for 24 hr and ChIP with p53
|
| Data processing |
Base-calling performed with CASAVA (Illumina).
Reads were aligned against the hg18 reference genome via Bowtie (v0.12.2), requiring mapping to unique genomic locations and allowing up to 2 mismatches.
Peaks were called via SISSRs using default settings, with input DNA used as a control (p<0.0001).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read coverage is represented in wig format; scores respresent uniquely-mapped non-redundant reads in 200bp bins, normalized by 10,000,000 divided by total uniquely-mapped non-redundant read counts per sample.
Supplementary_files_format_and_content: Peak calls from SISSRs were converted to coordinate ranges in standard BED format.
|
| |
|
| Submission date |
May 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE46641 |
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (ChIP-seq) |
| GSE46642 |
Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells |
|
| Relations |
| BioSample |
SAMN02117600 |
| SRA |
SRX275504 |
