Comment[ArrayExpressAccession]	E-GEOD-53965						
MAGE-TAB Version	1.1						
Public Release Date	2014-05-15						
Investigation Title	Global analysis of p53-regulated transcription reveals its direct targets and unexpected regulatory mechanisms (microarray)						
Comment[AEExperimentDisplayName]	Transcription profiling by array of human HCT116 cells treated with Nutlin-3 (an inhibitor of mdm2 and p53 interaction) or DMSO control to study p53-regulated transcription						
Comment[Submitted Name]	Global analysis of p53-regulated transcription reveals its direct targets and unexpected regulatory mechanisms (microarray)						
Experiment Description	HCT116 microarray done 12 hours after treatment with DMSO (control) or Nutlin Total RNA from HCT116 cells was harvested with an RNeasy kit (Qiagen) and analyzed on Affymetrix HuGene 1.0 ST arrays following the manufacturer’s instructions. Microarray data were processed using Partek Genomics Suite 6.6. Anova was used to call differentially expressed genes for which any isoform showed a fold change > |+/-1.5| with FDR <0.05. There were 362 genes called as upregulated and 367 genes as downregulated.						
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	Allen	Allen	Dowell	Espinosa			
Person First Name	Mary	Mary	Robin	Joaquin			
Person Mid Initials	Ann	A	D				
Person Email	mary.a.allen@colorado.edu						
Person Affiliation	University of Colorado						
Person Phone	608-209-6921						
Person Address	BioFrontiers, University of Colorado, UCB 596  JSCBB, Boulder, Co, USA						
Person Roles	submitter						
Protocol Name	P-GSE53965-1	P-GSE53965-5	P-GSE53965-6	P-GSE53965-2	P-GSE53965-3	P-GSE53965-4	P-GSE53965-7
Protocol Description	Partek. 1. Import CEL files (Nutlin-3, replicates 1-3; DMSO, replicates 1-3)   a. Use Partek default RMA import settings  2. Add a categorical attribute (found under Workflows, Gene Expression, Import, Add sample attributes)  a. Attribute Name: Treatment  i. Group 1 Name: Nutlin  ii. Group 2 Name: DMSO  3. Detect differentially expressed genes (found under Workflows, Gene Expression, Analysis, Detect differentially expressed genes)  a. Add Factor: Treatment  b. Add Contrast  i. Group 1: Nutlin  ii. Group 2: DMSO  c. Output file saved as:   i. ANOVA - 120612  4. Create Gene Lists (found under Tools, Create Gene List)  a. Cutoffs:  Fold change > |+/-1.5|, p-value with FDR <0.05  b. Output files saved as:   i. Gene List - Increase 1_5 fold - FDR 0_05 – 120612  1. 413 genes up, 45 with no gene symbol = 368 genes  ii. Gene List - Decrease 1_5 fold - FDR 0_05 - 120612   1. 407 genes down, 25 with no gene symbol = 382 genes  5. Save ANOVA and Gene Lists in txt format ID_REF =  VALUE = log2 RMA signal	followd the affymetrix insructions in GeneChip(r) WT Terminal Labeling and Hybridization User Manual for use with the Ambion(r) WT Expression Kit	followd the affymetrix insructions in GeneChip(r) WT Terminal Labeling and Hybridization User Manual for use with the Ambion(r) WT Expression Kit	12 hours 10microM Nutlin-3 vs DMSO	HCT116 cells were grown in McCoy's 5A and passaged the day prior to treatment. Cells were plated at a concentration of 300,000 cells per well of 6 well plate and treated 24 hours later with either Nutlin-3R (10uM) or the equivalent amount of vehicle (DMSO) for 12 hour.	Total RNA was harvested with an RNeasy kit (Qiagen)	followed the affymetic manual GeneChip(r) Expression Wash, Stain and Scan User Manual For Cartridge Arrays
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	compound	dose					
Experimental Factor Type	compound	dose					
Comment[SecondaryAccession]	GSE53965						
Comment[GEOReleaseDate]	2014-05-15						
Comment[ArrayExpressSubmissionDate]	2014-01-09						
Comment[GEOLastUpdateDate]	2014-05-17						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE53965_ANOVA-120612.TXT						
SDRF File	E-GEOD-53965.sdrf.txt