Comment[ArrayExpressAccession]	E-GEOD-50933						
MAGE-TAB Version	1.1						
Public Release Date	2013-11-19						
Investigation Title	Essential functions for ID proteins at multiple checkpoints in natural killer T cell development						
Comment[Submitted Name]	Essential functions for ID proteins at multiple checkpoints in natural killer T cell development						
Experiment Description	Thymic iNKT cell development is divided into four stages (stage 0-3) that are characterised, in C57BL/6 mouse strain, by the differential expression of surface markers, such as CD24, CD44 and NK1.1. During transition from immature to mature iNKT cell subsets, gene expression is tightly regulated. Here, we used microarray analysis to detail the influence of the transcriptional regulator ID3 during iNKT cell maturation in the thymus. Stage 1 (Tet+CD24-CD44-NK1.1-) and Stage 2 (Tet+CD24-CD44+NK1.1-) iNKT cells from WT and Id3KO thymi were FACS sorted for RNA extraction and Affymetrix hybridisation.						
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	Kee	Kee	Sigvardsson				
Person First Name	Barbara	Barbara	Mikael				
Person Mid Initials	L	L					
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	The University of Chicago						
Person Address	Pathology, The University of Chicago, 924 E57th st, Chicago, Illinois, USA						
Person Roles	submitter						
Protocol Name	P-GSE50933-1	P-GSE50933-5	P-GSE50933-6	P-GSE50933-2	P-GSE50933-3	P-GSE50933-4	P-GSE50933-7
Protocol Description	Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization. ID_REF =  VALUE = RMA adjusted natural log signal intensity	Biotinylated cRNA was prepared according to the Affymetrix two-cycle cDNA sunthesis.	10 ug of fragmented cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.	Thymocyte single cell suspensions were surface stained and FACS sorted into RLT-containing (Qiagen) eppendorf tubes, before freezing in dry ice. Cells were stored in -80C until RNA extraction was performed.	Mice were housed at the Univeristy of Chicago Animal Resource Center, following the guidelines of The University of Chicago Institutional Animal Care and Use Committee.	RNA was prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.	Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.
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	cell type	genotype					
Experimental Factor Type	cell type	genotype					
Comment[SecondaryAccession]	GSE50933						
Comment[GEOReleaseDate]	2013-11-19						
Comment[ArrayExpressSubmissionDate]	2013-09-17						
Comment[GEOLastUpdateDate]	2013-11-21						
Comment[AEExperimentType]	transcription profiling by array						
Pubmed ID	24244015						
Publication DOI	10.4049/jimmunol.1301521						
Publication Title	Essential functions for ID proteins at multiple checkpoints in invariant NKT cell development						
Publication Author List	Verykokakis M, Krishnamoorthy V, Iavarone A, Lasorella A, Sigvardsson M, Kee BL						
SDRF File	E-GEOD-50933.sdrf.txt