Comment[ArrayExpressAccession]	E-GEOD-46091
MAGE-TAB Version	1.1						
Public Release Date	2013-04-17
Investigation Title	Genes regulated by the gamma secretase inhibitor in WT and Ikaros deficient DN3 cells						
Comment[Submitted Name]	Genes regulated by the gamma secretase inhibitor in WT and Ikaros deficient DN3 cells
Experiment Description	Lineage-negative thymocytes were cultured on OP9-DL1 stromal cells for 16h in the presence of DMSO or the gamma secretase inhibitor MRK-003. DN3 cells cells were then sorted and their transcriptome analyzed. 8 samples						
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	Chan	Kastner					
Person First Name	Susan	Philippe					
Person Email	scpk@igbmc.fr						
Person Affiliation	IGBMC						
Person Phone	33 3 88 65 34 72						
Person Fax	33 3 88 65 32 01						
Person Address	IGBMC, 1, rue Laurent Fries, Illkirch, France						
Person Roles	submitter						
Protocol Name	P-GSE46091-1	P-GSE46091-5	P-GSE46091-6	P-GSE46091-2	P-GSE46091-3	P-GSE46091-4	P-GSE46091-7
Protocol Description	CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities. ID_REF =  VALUE = log2 RMA signal	Biotinylated cRNA targets were prepared according to Affymetrix recommendations in GeneChip Expression Analysis Technical Manual (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA in a two cycle target labeling assay.	10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).	Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.	Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.	DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.	The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.
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	TREATMENT	VARIATION					
Experimental Factor Type	treatment	variation					
Comment[SecondaryAccession]	GSE46091						
Comment[GEOReleaseDate]	2013-04-17						
Comment[ArrayExpressSubmissionDate]	2013-04-16						
Comment[GEOLastUpdateDate]	2013-04-18						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-46091.sdrf.txt