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Sample GSM1133485 Query DataSets for GSM1133485
Status Public on Jul 01, 2013
Title U2OS_DXR_input
Sample type SRA
Source name U2OS cell line
Organism Homo sapiens
Characteristics cell type: U2OS
cell type: osteosarcoma
treatment: 0.6 ug/ml Doxorubicin for 24 hr
chip antibody: none
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 cells treated with 0.6 ug/ml Doxorubicin for 24 hr
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
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
BioSample SAMN02117599
SRA SRX275503

Supplementary file Size Download File type/resource
GSM1133485_U2OS_DXR_input.normalized.variableStep.wig.gz 31.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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