Comment[ArrayExpressAccession]	E-GEOD-46240
MAGE-TAB Version	1.1				
Public Release Date	2013-04-21
Investigation Title	Global genomic profiling of p53-regulated genes				
Comment[Submitted Name]	Global genomic profiling of p53-regulated genes
Experiment Description	p53 is a critical tumor suppressor and works as a stress-induced transcription factor to induce target genes mediating apoptosis, cell cycle arrest and senescence or other responses. To gain new insights into p53 biology, we used high-throughput sequencing to analyze global p53 transcriptional networks in primary mouse embryo fibroblasts in response to DNA damage. ChIP-sequencing reveals 4785 p53-bound sites in the genome located near 3193 genes involved in diverse biological processes. RNA-sequencing analysis shows that only a subset of p53-bound genes is transcriptionally regulated, yielding a list of 432 p53-bound and regulated genes. Furthermore, we define a list of 1269 basal-p53 regulated genes, of which 253 are p53-bound and basal-p53 regulated. ChIP-seq was performed to determine the genome-wide p53 binding sites in doxorubicin-treated primary MEFs. RNA-seq was used to define differentially expressed genes in response to DNA damage in wild-type and p53-/- MEFs, and basal p53 regulated genes by deriving differentially expressed genes between untreated wild-type and p53-/- MEFs.				
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	Spano Mello	Kenzelmann Broz	Attardi		
Person First Name	Stephano	Daniela	Laura		
Person Mid Initials			D		
Person Email	geo@ncbi.nlm.nih.gov				
Person Affiliation	Stanford University				
Person Address	Stanford University, 269 Campus Drive, Stanford, CA, USA				
Person Roles	submitter				
Protocol Name	P-GSE46240-4	P-GSE46240-1	P-GSE46240-5	P-GSE46240-3	P-GSE46240-2
Protocol Description	ChIP-seq and RNA-seq reads were aligned to the mm9 genome assembly using DNAnexus. For ChIP-seq: Peaks were called using the DNAnexus ChIP-seq analyses tool with the following specifications: peak enrichment >20, peak-to background enrichment >3, a minimum ratio between uniquely and repetitively mapped reads of 3:1, a kernel bandwith of 30.0, FDR calculation enabled. Background was combined input reads and reads from p53 ChIP in p53-/- MEFs. For RNA-seq: Tag counts were derived using the DNAnexus 3SEQ transcriptome-based quantification tool with the following specifications: Sense only, RefSeq genes. The DESeq library was used to normalize tag counts between samples and to call differentially expressed genes. Genome_build: mm9 Supplementary_files_format_and_content: ChIP-seq: Processed data files are tab-delimited text files containing 1) Chromosome name, 2) Position (summit of the peak), 3) enrichment (based on background reads), 4) neg_log10_qvalue (negative log of q-value of peak) and 5) peak rank. Supplementary_files_format_and_content: RNA-seq: Processed files are tab-delimited text files containing normalized gene expression, obtained using DESeq.	untreated or 0.2ug/ml doxorubicin for 6h	For RNA-seq, total RNA was isolated using Trizol reagent, and mRNA was purified with the Dynabeads mRNA Purification Kit from Invitrogen. For RNA-seq, libaries were prepared according to the 3-seq protocol: RNA was heat-sheared to fragments of 100-200 bp followed by first and second strand synthesis, linker ligation, size selection on agarose gel and PCR amplification for 15 cycles.	For ChIP-seq, samples were prepared according to Myers lab ChIP-seq protocol: cells were cross-linked with 1% formaldehyde at room temperature for 10 min, cells were extracted with Farnham and RIPA buffers, and chromatin was fragmented by sonication. For ChIP-Seq, libraries were prepared according to the Illumina ChIP-seq library preparation protocol: ChIP DNA was blunt ended, ligated to Solexa adaptors, amplified using adaptor primers and size-selected on agarose gel.	DMEM with 10% FCS, for ChIP-seq 4x106 cells were plated on 15 cm dish one day prior to treatment, for RNA-seq 1.5x 106 cells were plated on 10 cm dish
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	TREATMENT	CHIP ANTIBODY	GENOTYPE		
Experimental Factor Type	treatment	chip antibody	genotype		
Publication Title	Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses.				
Publication Author List	Kenzelmann Broz D, Spano Mello S, Bieging KT, Jiang D, Dusek RL, Brady CA, Sidow A, Attardi LD				
PubMed ID	23651856				
Publication DOI	10.1101/gad.212282.112				
Comment[SecondaryAccession]	GSE46240				
Comment[GEOReleaseDate]	2013-04-21				
Comment[ArrayExpressSubmissionDate]	2013-04-20				
Comment[GEOLastUpdateDate]	2013-06-03				
Comment[AEExperimentType]	ChIP-seq				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[AdditionalFile:Data1]	GSE46240_ChIP-seq_peaks_p53_binding_sites.txt				
Comment[SecondaryAccession]	SRP021219				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR832846-SRR832859				
SDRF File	E-GEOD-46240.sdrf.txt