Investigation Title	Transcription profiling time series of gene expression following irradiation to identify P53 activity						
Comment[Submitted Name]	Hubank Human MOLT4 Irradiation						
Experimental Design	stimulus_or_stress_design	time_series_design	transcription profiling by array				
Experimental Design Term Source REF	mo	mo	EFO				
Comment[AEExperimentType]	transcription profiling by array						
Comment[AEExperimentDisplayName]	Transcription profiling by array of irradiated human MOLT4 cells						
Comment[ArrayExpressReleaseDate]	2006-03-01						
Comment[AEMIAMESCORE]	5						
Comment[ArrayExpressAccession]	E-MEXP-549						
Comment[MAGETAB TimeStamp_Version]	2010-08-11 15:16:01 Last Changed Rev: 13058						
Experimental Factor Name	time	irradiate	dose				
Experimental Factor Type	time	irradiate	dose				
Experimental Factor Term Source REF							
Person Last Name	Barenco	Stark	hubank	Hubank	Tomescu	Callard	Brewer
Person First Name	Martino	Jaroslav	mike	Michael	Daniela	Robin	Daniel
Person Mid Initials			j				
Person Email			m.hubank@ich.ucl.ac.uk				
Person Phone			2079052266				
Person Fax							
Person Address			30, Guilford St				
Person Affiliation	ICH, University College Londoon	Imperial College London	ICH Gene Microarray Centre	ICH, University College Londoon	ICH, University College Londoon	ICH, University College Londoon	ICH, University College Londoon
Person Roles			submitter				
Person Roles Term Source REF							
Quality Control Type	biological_replicate						
Quality Control Term Source REF	The MGED Ontology						
Replicate Type							
Replicate Term Source REF							
Normalization Type							
Normalization Term Source REF							
Date of Experiment							
Public Release Date	2006-03-01						
PubMed ID	16584535						
Publication DOI	10.1186/gb-2006-7-3-r25						
Publication Author List	Martino Barenco; Daniela Tomescu; Daniel Brewer; Robin Callard; Jaroslav Stark; Michael Hubank						
Publication Title	Ranked Prediction of p53 Targets Using Hidden Variable Dynamic Modelling (HVDM).						
Publication Status	published						
Publication Status Term Source REF	EFO						
Experiment Description	The purpose of the experiment was to generate a time course of gene expression following irradiation. The goal was then to model this data to extract hidden variables - chiefly, the activity profiles of the p53 transcription factor. Using this information the aim was to predict which transcripts changed by IR were targets of p53.  Cells in log phase (1 x 106 ml-1) were ?-irradiated with 5 Gy at room temperature (RT) at a dose rate of 2.45 Gy per minute with a 137Cs ?-irradiator. Cells were harvested at 0, 2, 4, 6, 8, 10 and 12 hours, and RNA and protein were extracted (Trizol, Invitrogen). Affymetrix U133A arrays were hybridized as standard (www.affymetrix.co.uk). Array quality was determined using R and GCOS .rpt file values. The time course was replicated three times from independent cell preparations.						
Protocol Name	P-MEXP-16843	P-MEXP-16844	P-MEXP-16845	P-MEXP-9419	Affymetrix:Protocol:Hybridization-EukGE-WS2v4	P-AFFY-6	Affymetrix:Protocol:ExpressionStat
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	feature_extraction	bioassay_data_transformation
Protocol Description	Human MOLT4 cells (T cell acute lymphoblastic leukaemia) were obtained from NIBSC, UK (CFARP011) and cultured in RPMI, 10% FCS, L-glutamine, plus antibiotics.	Cells in log phase (1 x 106 ml-1) were gamma-irradiated with 5 Gy at room temperature (RT) at a dose rate of 2.45 Gy per minute with a 137Cs gamma-irradiator. Cells were harvested at 0, 2, 4, 6, 8, 10 and 12 hours, and RNA and protein were extracted (Trizol, Invitrogen). RNA and cRNA quantity and quality was determined by Nanodrop spectophotometer and Bioanalyser 2100 (Agilent). Affymetrix U133A arrays were hybridized as standard (www.affymetrix.co.uk). Array quality was determined using R and GCOS .rpt file values. 	30 ml of MOLT4 cells in log phase (2 x 10e6 ml-1) were centrifuged (400g, 5 min) and lysed with 5 ml Trizol. RNA was purified according to the TRIZOL protocol (Invitrogen). RNA was precipitated with propanol, washed with 70% ethanol and resuspended in 80ul water.	Standard Affymetrix	Title: Fluidics Station Protocol. Description: 	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description: 
Protocol Parameters	max temperature;min temperature;		Extracted product;Amplification;	Label used;Amplification;			
Protocol Hardware							
Protocol Software					MicroArraySuite 5.0	MicroArraySuite 5.0	MicroArraySuite 5.0
Protocol Contact							
Protocol Term Source REF		mo					The MGED Ontology
SDRF File	E-MEXP-549.sdrf.txt						
Term Source Name	ncbitax		ArrayExpress	The MGED Ontology	mo	EFO	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html		http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	
Term Source Version