Comment[ArrayExpressAccession]	E-GEOD-39761
MAGE-TAB Version	1.1						
Public Release Date	2013-12-01
Investigation Title	CD8+ T cell gene expression after different antigen dose stimulations						
Comment[Submitted Name]	CD8+ T cell gene expression after different antigen dose stimulations
Experiment Description	This study aimed to identify the human T cell response toward different antigen doses. Fresh isolated CD8+ T cells from peripheral blood mononuclear cells (PBMCs) were stimulated with influenza M1 peptide-loaded autologous monocyte-derived dendritic cells for 2 weeks. A high M1 peptide antigen dose (10uM on moDC, HD1-5) and an optimal antigen dose (10nM on moDC OD1-5) were used. M1-specific CD8 T cells were tetramer sorted at the end of the 2 weeks. RNA was extracted and analyzed for gene expression using Agilent 8X60K gene expression microarrays. 5 independent samples from 3 different HLA A2+ blood donors.						
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	Chiu	Chiu	Schneck				
Person First Name	Yen-Ling	Yen	Jonathan				
Person Mid Initials		L	P				
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	Johns Hopkins University						
Person Address	Johns Hopkins University, 733 N. Broadway, BRB 615, Baltimore, MD, USA						
Person Roles	submitter						
Protocol Name	P-GSE39761-1	P-GSE39761-5	P-GSE39761-6	P-GSE39761-2	P-GSE39761-3	P-GSE39761-4	P-GSE39761-7
Protocol Description	The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities were normalized by dividing the intensity values by their median. ID_REF =  VALUE = Normalized signal intensity	To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer.	The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.	Different peptide doses were used to pulse dendritic cells (optimal dose: 10nM; high dose: 10uM).	CD8+ T cells were stimulated with M1 peptide-pulsed monocyte-derived dendritic cells in complete RPMI media supplemented with T cell growth factor.	T cells were harvested on D14 and tetramer sorted before Trizol-based RNA extraction.	Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).
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	PEPTIDE DOSAGE						
Experimental Factor Type	peptide dosage						
Comment[SecondaryAccession]	GSE39761						
Comment[GEOReleaseDate]	2013-12-01						
Comment[ArrayExpressSubmissionDate]	2012-07-30						
Comment[GEOLastUpdateDate]	2013-12-01						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-39761.sdrf.txt