Comment[ArrayExpressAccession]	E-GEOD-45955
MAGE-TAB Version	1.1						
Public Release Date	2013-10-08
Investigation Title	Differential requirement for Nfil3 during NK cell development						
Comment[Submitted Name]	Differential requirement for Nfil3 during NK cell development
Experiment Description	Nfil3 has multiple functions during conventional NK cell and thymic NK cell development. Nfil3 controls NK cell development from the earliest committed NK cell progenitor stage. Nfil3-/- prepro NK cells retained T-cell potential due to the failure to repress T cell specific genes. At later stages of NK cell development, Nfil3 regulates the formation of mature NK cells by promoting directly or indirectly the expression of transcription factor Eomes. We also demonstrate that Nfil3 is important for thymic NK cell development whereas Trail+ immature NK cells generated in the bone marrow of neonates and in the adult liver develop independent of Nfil3 function. We used microarrays to analyse the changes in gene expression due to the presence or absence of Nfil3, both in prepro NK cells and ALP cells (all lymphoid progenitors) Samples were obtained on two experimentation dates. Replicate 1 was processed in April 2012, replicate 2 was processed in May 2012.						
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	Core	Seillet	Carotta				
Person First Name	Victoria	Cyril	Sebastian				
Person Email	victoria@dnaarrays.org						
Person Affiliation	Institute for Research in Biomedicine						
Person Address	Functional Genomics Core, Institute for Research in Biomedicine, Baldiri Reixac, 10, Barcelona, Spain						
Person Roles	submitter						
Protocol Name	P-GSE45955-1	P-GSE45955-5	P-GSE45955-6	P-GSE45955-2	P-GSE45955-3	P-GSE45955-4	P-GSE45955-7
Protocol Description	CEL files were generated from images (DAT files) using Command Console (Affymetrix, Santa Clara, CA), log2 RMA expression estimates were calculated using Partek Genomics Suite ID_REF =  VALUE = log2 RMA expression estimate	RNA was amplified for 23 cycles using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), as described in Gonzalez Roca et al. 2012.	8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)	cells were flow cytometrically isolated from lineage depleted bone marrow derived from ID2-GFP reporter mice and immediately lysed for RNA purification.	freshly isolated progenitor cells from lineage depleted bone marrow of ID2-GFP reporter were analysed. Cells were not cultivated prior RNA isolation.	RNA was extracted using Agencourt RNAClean XP magnetic beads (Beckman Coulter) as described (Gonzalez Roca et al. 2010)	GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)
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	DATE	CELL TYPE	GENOTYPE				
Experimental Factor Type	date	cell type	genotype				
Comment[SecondaryAccession]	GSE45955						
Comment[GEOReleaseDate]	2013-10-08						
Comment[ArrayExpressSubmissionDate]	2013-04-10						
Comment[GEOLastUpdateDate]	2013-10-08						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-45955.sdrf.txt