Comment[ArrayExpressAccession]	E-GEOD-42922
MAGE-TAB Version	1.1							
Public Release Date	2013-02-11
Investigation Title	TCR affinity-dependent functional inhibition via PD-1 and SHP-1 phosphatase							
Comment[Submitted Name]	TCR affinity-dependent functional inhibition via PD-1 and SHP-1 phosphatase
Experiment Description	To investigate gene expression changes associated with stimulation of TCRs of different affinity, primary CD8 T cells were transduced with sequence optimized TCRs of various affinities and stimulated for 6h. Gene expression was measured at baseline (0h) and after 6h after stimulation with low dose NY-ESO-1 multimer							
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	Baitsch	Rufer	Hebeisen	Baitsch				
Person First Name	Lukas	N	M	L				
Person Email	lukas_baitsch@dfci.harvard.edu							
Person Affiliation	Dana Farber Cancer Institute							
Person Address	Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, USA							
Person Roles	submitter							
Protocol Name	P-GSE42922-1	P-GSE42922-6	P-GSE42922-3	P-GSE42922-8	P-GSE42922-7	P-GSE42922-2	P-GSE42922-4	P-GSE42922-5
Protocol Description	ID_REF =  VALUE = normalized signal intensity	Hybridization was performed according to manufacturer recommendations to Agilent Whole Human Genome Oligo Microarrays (4x44k).	primary CD8 T cells were transduced with sequence-optimized NY-ESO-1 specific TCR variants and cultivated in RPMI + 8% HS + 10U/ml rhIL-2 for 24h	data was obtained using the Feature Extraction Software version v.9.1. Background correction, Normalization, and Filtering were done using the Agi4x44PreProcess software package for Bioconductor. The preinstalled thresholds for probe filtering were applied, which filter probes that do not fulfull the following criteria in at least 75% of the samples: (i) above detection limit, (ii) are found, (iii) above negative controls and (iv) are not saturated. After filtering, 33114 probes remaind in the dataset. The limma package was used to calculate differentially expressed genes.	Agilend microarray scanner system (Agilent).	cells were either left untreated (baseline, 0h) or were stimulated with 0.002ug/ml unlabeled NY-ESO-1(57-165)-specific multimer for 6h at 37 degrees celsius	After incubation, cells were washed with ice-cold PBS and then quick frozen in liquid nitrogen. RNA extraction was isolated using NucleoSpin RNA II extraction protocol (MN).	1ug RNA was amplified using a T7-based amplification protocol and labeled with Cyanine 3 (Cy3).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	STIMULATED WITH	TRANSDUCED WITH	AFFINITY					
Experimental Factor Type	stimulated with	transduced with	affinity					
Publication Title	SHP-1 phosphatase activity counteracts increased T cell receptor affinity.							
Publication Author List	Hebeisen M, Baitsch L, Presotto D, Baumgaertner P, Romero P, Michielin O, Speiser DE, Rufer N							
PubMed ID	23391724							
Publication DOI	10.1172/JCI65325							
Comment[SecondaryAccession]	GSE42922							
Comment[GEOReleaseDate]	2013-02-11							
Comment[ArrayExpressSubmissionDate]	2012-12-14							
Comment[GEOLastUpdateDate]	2013-02-11							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-42922.sdrf.txt