Investigation Title	Transcription profiling of wild type and aire -/- murine meduallary thymic epithelial cells to study the immunological roles of aire protein in thymus.						
Comment[Submitted Name]	wild type and aire -/- murine meduallary thymic epithelial cells						
Experimental Design	individual_genetic_characteristics_design	co-expression_design	transcription profiling by array				
Experimental Design Term Source REF		mo	EFO				
Comment[AEExperimentType]	transcription profiling by array						
Comment[AEExperimentDisplayName]	Transcription profiling by array of mice mutant for aire						
Comment[ArrayExpressReleaseDate]	2007-12-15						
Comment[SecondaryAccession]	GSE85						
Comment[AEMIAMESCORE]	5						
Comment[SecondaryAccession]	GDS167						
Comment[ArrayExpressAccession]	E-GEOD-85						
Comment[MAGETAB TimeStamp_Version]	2010-08-09 10:22:24 Last Changed Rev: 13058						
Experimental Factor Name	genotype						
Experimental Factor Type	genotype						
Experimental Factor Term Source REF							
Person Last Name	Lab						
Person First Name	CBDM						
Person Mid Initials	Z.						
Person Email	cbdm@joslin.harvard.edu						
Person Phone							
Person Fax							
Person Address	CBDM, Immunology and Immunogenetics, Joslin Diabetes Center, One Joslin Place, Boston, 02215, USA						
Person Affiliation	Joslin Diabetes Center						
Person Roles	submitter						
Person Roles Term Source REF	The MGED Ontology						
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	2007-12-15						
PubMed ID	12376594						
Publication DOI	10.1126/science.1075958 						
Publication Author List	Mark S Anderson, Emily S Venanzi, Ludger Klein, Zhibin Chen, Stuart P Berzins, Shannon J Turley, Harald von Boehmer, Roderick Bronson, Andrée Dierich, Christophe Benoist, Diane Mathis						
Publication Title	Projection of an immunological self shadow within the thymus by the aire protein.						
Publication Status	published						
Publication Status Term Source REF	EFO						
Experiment Description	Mice used were B6/129 F2's, 3-5 weeks of age, either wild type or with both copies of the autoimmune regulator gene (aire, GenBank #AF079536) disrupted.  Thymi from five of these mice of both sexes were removed and pooled. After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them. RNA was twice-amplified using a T7 polymerase-based method.						
Protocol Name	Affymetrix:Protocol:Hybridization-Unknown	P-AFFY-6					
Protocol Type	hybridization	feature_extraction					
Protocol Description	Title: Affymetrix Generic Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 					
Protocol Parameters							
Protocol Hardware							
Protocol Software	MicroArraySuite 5.0	MicroArraySuite 5.0					
Protocol Contact							
Protocol Term Source REF	mo						
SDRF File	E-GEOD-85.sdrf.txt						
Term Source Name	NCI_thesaurus	The MGED Ontology		ArrayExpress	mo	EFO	The MGED Ontology
Term Source File	ncithesaurus.obo.alt	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