Comment[ArrayExpressAccession]	E-GEOD-44963
MAGE-TAB Version	1.1								
Public Release Date	2014-03-01
Investigation Title	Expression data from BCG-immunized monkey PBMCs stimulated with lipid antigen								
Comment[Submitted Name]	Expression data from BCG-immunized monkey PBMCs stimulated with lipid antigen
Experiment Description	The role of CD1-restricted, lipid-specific T cells in vivo remains to be elucidated. We used microarrays to detail the global program of gene expression accompanied by the activation of CD1-restricted, lipid-specific T cells. Monkeys were immunized with BCG bacteria to evoke CD1-restricted, mycolyl glycolipid-specific T cell responses at high frequency. The PBMCs were stimulated in the presense or absense of mycolyl glycolipid antigen, followed by RNA extraction and hybridization on Affymetrix microarrays.								
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	Morita	Morita	Miyamoto	Ichise	Hattori	Nakamura	Igarashi	Harashima	Sugita
Person First Name	Daisuke	Daisuke	Ayumi	Hiroshi	Yuki	Takashi	Tatsuhiko	Hideyoshi	Masahiko
Person Email	geo@ncbi.nlm.nih.gov								
Person Affiliation	Kyoto-university								
Person Address	Institute for virus research, Kyoto-university, 53 Shogoin Kawara-cho, Sakyo-ku, Kyoto, Japan								
Person Roles	submitter								
Protocol Name	P-GSE44963-1	P-GSE44963-4	P-GSE44963-5	P-GSE44963-2	P-GSE44963-3	P-GSE44963-6			
Protocol Description	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. ID_REF =  VALUE = MAS5.0 ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.	monkey PBMCs were stimulated in the presense or absense of GMM for 24hr.	Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.	GeneChips were scanned using the GeneChip Scanner 3000 ７G.			
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol			
Experimental Factor Name	STIMULATED WITH								
Experimental Factor Type	stimulated with								
Comment[SecondaryAccession]	GSE44963								
Comment[GEOReleaseDate]	2014-03-01								
Comment[ArrayExpressSubmissionDate]	2013-03-07								
Comment[GEOLastUpdateDate]	2014-03-01								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-44963.sdrf.txt