Comment[ArrayExpressAccession]	E-GEOD-40875
MAGE-TAB Version	1.1							
Public Release Date	2013-03-17
Investigation Title	Early parity-induced gene expression in mouse mammary cell subtypes							
Comment[Submitted Name]	Early parity-induced gene expression in mouse mammary cell subtypes
Experiment Description	This study examined the effect of early pregnancy on the gene expression profiles of stromal and various epithelial mammary cell subpopulations in mice. Mammary cell subpopulations were isolated from parous and age-matched virgin control mice. Three independent replicates were assessed per cell subpopulation and treatment group, resulting in a total of 35 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	Roloff	Meier-Abt	Thiry	Roloff	Bentires-Alj			
Person First Name	Tim	Fabienne	Stephane	Tim	Mohamed			
Person Email	tim.roloff@fmi.ch							
Person Affiliation	FMI							
Person Address	Functional Genomics, FMI, Maulbeerstrasse 66, Basel, Switzerland							
Person Roles	submitter							
Protocol Name	P-GSE40875-1	P-GSE40875-6	P-GSE40875-3	P-GSE40875-8	P-GSE40875-7	P-GSE40875-2	P-GSE40875-4	P-GSE40875-5
Protocol Description	ID_REF =  VALUE = log2 transformed RMA normalized expression values	Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.	Mice were maintained according to the national guidelines.	Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the justRMA() function.	Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader	Mice were mated when 42 days old, allowed to undergo normal pregnancy and 21 and 40 days were allocated for lactation and mammary gland involution, respectively.	The 4th mammary glands from parous and age-matched virgin control mice were collected, digested to single cells and FACS-sorted into distinct mammary cell subpopulations.	total RNA from FACS sorted cells (2000 or 10000 depending on sample) was amplified using the NuGEN Ovation Pico WTA System (NuGEN # 3300). 3ug of the the resulting SPIA amplified cDNA was processed with the NuGEN WT-Ovation Exon Module. 5.5ug of the resulting ssDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	BIOLOGICAL REPLICATE	REPRODUCTIVE HISTORY	CELL TYPE					
Experimental Factor Type	biological replicate	reproductive history	cell type					
Comment[SecondaryAccession]	GSE40875							
Comment[GEOReleaseDate]	2013-03-17							
Comment[ArrayExpressSubmissionDate]	2012-09-14							
Comment[GEOLastUpdateDate]	2013-03-18							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-40875.sdrf.txt