Comment[ArrayExpressAccession]	E-GEOD-57047
MAGE-TAB Version	1.1				
Public Release Date	2014-10-26
Investigation Title	Expression data in antigen-specific CD8 T cells in the absence of ATG7				
Comment[Submitted Name]	Expression data in antigen-specific CD8 T cells in the absence of ATG7
Experiment Description	Autophagy genes play an important role in the T cell activation and proliferation. We examined the role of ATG7 during the process of CD8 T cell memory formation. In the absence of ATG7, antigen-specific CD8 T cells failed to survive past the contraction phase and failed to give rise to memory cells. We used microarrays to examine the global programme of gene expression underlying changes introduced in the absence of the ATG7 gene and identified distinct classes genes varied their expression during this time-point. Mouse LCMV-specific CD8 T cells were isolated at day 8 post LCMV infection for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare the gene expression profiles in wild-type cells and cells lacking the ATG7 gene during the peak of their expansion.				
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	Xu	Xiaojin	Koichi	Rafi	
Person First Name	Xiaojin	Xu	Araki	Ahmed	
Person Email	xiaojinxu@gmail.com				
Person Affiliation	Emory University School of Medicine				
Person Address	Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia, USA				
Person Roles	submitter				
Protocol Name	P-GSE57047-1	P-GSE57047-3	P-GSE57047-4	P-GSE57047-2	P-GSE57047-5
Protocol Description	The data were analyzed with Microarray Suiteusing Affymetrix default analysis settings and global scaling as normalization method. ID_REF =  VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	Biotinylated cDNA were prepared from NuGEN Ovation V2 Amplification System according to the standard protocol from total RNA.	Following fragmentation, cDNA were hybridized over-night at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.	QIAgen RNeasy Plus kit was used to extract total RNAs from the isolated cells according to manufacturer's instruction	GeneChips were scanned using a high resolution confocal scanner.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	genotype				
Experimental Factor Type	genotype				
Comment[SecondaryAccession]	GSE57047				
Comment[GEOReleaseDate]	2014-10-26				
Comment[ArrayExpressSubmissionDate]	2014-04-24				
Comment[GEOLastUpdateDate]	2014-10-26				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-57047.sdrf.txt