Comment[ArrayExpressAccession] E-GEOD-46992 MAGE-TAB Version 1.1 Public Release Date 2013-10-23 Investigation Title Genome-wide map of p53 binding sites by ChIP-seq in human lymphoblastoid cell lines treated with nutlin-3 Comment[Submitted Name] Genome-wide map of p53 binding sites by ChIP-seq in human lymphoblastoid cell lines treated with nutlin-3 Experiment Description We have used chromatin immune-precipitation with parallel sequencing (ChIP-Seq) technology to identify genome-wide p53 binding in human lymphoblastoid cell lines treated with a MDM2 inhibitor nutlin-3 ChIP-Seq analysis of p53 binding sites in human lymphoblastoid cells treated with nutlin-3 or vehicle Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Wang Campbell Wang Su Bell Person First Name Xuting Michelle Xuting Dan Douglas Person Mid Initials R A Person Email wang21@niehs.nih.gov Person Affiliation NIEHS/NIH Person Phone 9193164598 Person Address NIEHS/NIH, 111 TW Alexander Dr, Research Triangle Park, NC, USA Person Roles submitter Protocol Name P-GSE46992-4 P-GSE46992-1 P-GSE46992-3 P-GSE46992-2 Protocol Description Basecalls performed using CASAVA version 1.4 ChIP-seq reads were aligned to the hg18 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations Uniquely mapped reads with mis-match <= 2 were used for peak detection Peaks were called using QuEST (version 2.4) using the “Transcription factor binding site” setting (bandwidth of 30 bp, region size of 300 bp) and the “stringent peak calling” parameters (corresponding to 50-fold ChIP to input enrichment for seeding the regions, and 3-fold ChIP enrichment for extending the regions). Peaks with FDR q <= 0.05 Genome_build: hg19 human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 10 μM nutlin-3 (Sigma) or 0.1% (v/v) DMSO as a vehicle control for 18 hours Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with mouse monoclonal anti-human p53 (BD Pharmingen, cat# 554294). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols. human lymphoblastoid cells were grown as recommended by Coriell Protocol Type normalization data transformation protocol sample treatment protocol nucleic acid library construction protocol growth protocol Publication Title A Polymorphic p53 Response Element in KIT Ligand Influences Cancer Risk and Has Undergone Natural Selection. Publication Author List Zeron-Medina J, Wang X, Repapi E, Campbell MR, Su D, Castro-Giner F, Davies B, Peterse EF, Sacilotto N, Walker GJ, Terzian T, Tomlinson IP, Box NF, Meinshausen N, De Val S, Bell DA, Bond GL PubMed ID 24120139 Publication DOI 10.1016/j.cell.2013.09.017 Comment[SecondaryAccession] GSE46992 Comment[GEOReleaseDate] 2013-10-23 Comment[ArrayExpressSubmissionDate] 2013-05-15 Comment[GEOLastUpdateDate] 2013-10-23 Comment[AEExperimentType] ChIP-seq Comment[AdditionalFile:Data1] GSE46992_hg19.QuEST.p53_ChIP_LCL_nutlin3.narrowPeak.txt Comment[SecondaryAccession] SRP022843 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR851805-SRR851806 SDRF File E-GEOD-46992.sdrf.txt