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Sample GSM1133488 Query DataSets for GSM1133488
Status Public on Jul 01, 2013
Title U2OS_NT_p53chip
Sample type SRA
 
Source name U2OS cell line
Organism Homo sapiens
Characteristics cell type: U2OS
cell type: osteosarcoma
treatment: no treatment control 24 hr and ChIP with p53 (control for Doxorubicin-treated cells)
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 37ÂșC 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 No Treatment control 24 hr and ChIP with p53 (control for Doxorubicin-treated cells)
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 SAMN02117602
SRA SRX275506

Supplementary file Size Download File type/resource
GSM1133488_U2OS_NT_p53chip.normalized.variableStep.wig.gz 22.7 Mb (ftp)(http) WIG
GSM1133488_U2OS_NT_p53chip.peakcalls.bed.gz 3.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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