Investigation Title	Transcription profiling of human head and neck squamous cell carcinomas to identify metastasis predictors and descriptors, and differentiation classifiers	
Comment[Submitted Name]	CIT-HS-HNSCC-BWK	
Experimental Design	disease_state_design	co-expression_design	transcription profiling by array	
Experimental Design Term Source REF	mo	mo	EFO	
Comment[ArrayExpressReleaseDate]	2007-08-23	
Comment[SecondaryAccession]		
Comment[AEMIAMESCORE]	5	
Comment[ArrayExpressAccession]	E-TABM-302	
Comment[MAGETAB TimeStamp_Version]	2010-08-12 17:46:17 Last Changed Rev: 13058	
Experimental Factor Name	DiseaseStaging	OrganismPart	Age	LymphNodeStage	DifferentiationState	
Experimental Factor Type	disease_staging	organism_part	age	lymph_node_stage	differentiation_state	
Experimental Factor Term Source REF	
Person Last Name	Petel	
Person First Name	Fabien	
Person Mid Initials	
Person Email	petelf@ligue-cancer.net	
Person Phone	
Person Fax	
Person Address	
Person Affiliation	Ligue Nationale Contre le Cancer	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2007-08-23	
PubMed ID	18679425	
Publication DOI	18679425	
Publication Author List	Rickman DS, Millon R, De Reynies A, Thomas E, Wasylyk C, Muller D, Abecassis J, Wasylyk B	
Publication Title	Prediction of future metastasis and molecular characterization of head and neck squamous-cell carcinoma based on transcriptome and genome analysis by microarrays	
Publication Status	journal_article	
Publication Status Term Source REF	
Experiment Description	A "Cartes d'Identite des Tumeurs" (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net). 81 samples on Affymetrix HG-U133 Plus 2.0 GeneChips arrays for 81 patients with primary Head and Neck Squamous Cell Carcinoma (HNSCC; oral cavity, tongue, oro- or hypopharynx); metastases as first recurrent event in a 36-month follow up; histologically tumor-free margins (?3 mm); patients had undergone surgical resection as the first treatment and had no clinically evident distant metastases. 	
Protocol Name	P-TABM-1651	P-TABM-1647	P-TABM-1649	Affymetrix:Protocol:Hybridization-EukGE-WS2v5	P-TABM-1648	P-AFFY-6	Affymetrix:Protocol:ExpressionStat	
Protocol Type	store	nucleic_acid_extraction	labeling	hybridization		feature_extraction	bioassay_data_transformation	
Protocol Description	samples stored at -80 C	RNA extraction using RNeasy extraction kit, Ref 74104 (Qiagen). RNAs were quantified using a spectrophotometer at 260 nm (Nanodrop). The quality of RNA was controlled by gel electrophoresis followed by staining with ethidium bromide and an Agilent 2100 Bioanalyser. RNAs were qualified if the 28S/18S ratio was more than 1.5 for Affymetrix experiments.	3 ug of total RNA of each sample as starting material.Enzo BioArray High Yield RNA Transcript Labeling kit, Affymetrix, P/N 900182; T7 RNA polymerase; one-cycle target labeling protocol; see http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf; one-cycle EukGE-WS2v5 target labeling protocol	Title: Affymetrix EukGE-WS2v5 Hybridization. Description: 	20 ug cRNA per Hybridization; In vitro transcription with Enzo BioArray High Yield RNA Transcript Labeling kit, Affymetrix, P/N 900182; Incubation under rotation (60 rpm); GeneChip Fluidics Station 400; Affymetrix HG-U133 Plus 2.0 GeneChip arrays	Title: Affymetrix CEL analysis. Description: 	Title: Affymetrix CHP Analysis (ExpressionStat). Description: 	
Protocol Parameters	temperature;	product;	amount of nucleic acid labeled;label used;amplification;	
Protocol Hardware	
Protocol Software				MicroArraySuite 5.0		MicroArraySuite 5.0	MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF							The MGED Ontology	
SDRF File	E-TABM-302.sdrf.txt	
Term Source Name	mo	EFO		nci_thesaurus	nci_meta	The MGED Ontology	ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/		http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do	http://ncimeta.nci.nih.gov/indexMetaphrase.html	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version