Comment[ArrayExpressAccession]	E-GEOD-42217
MAGE-TAB Version	1.1												
Public Release Date	2012-11-14
Investigation Title	yeast wt pool - plate reader												
Comment[Submitted Name]	yeast wt pool - plate reader
Experiment Description	Contains a collection of wildtype Saccharomyces cerevisiae strains for estimating the biological variation. Wildtypes are obtained from the yeast wildtypes – platereader, wt pool background set HybSet, by randomly taking 100 wt vs. refpool (pooled wts) and 100 refpool vs. wt hybridizations Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays.												
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	Kemmeren	van Leenen	Groot Koerkamp	van Hooff	Lijnzaad	Kemmeren	Holstege						
Person First Name	Patrick	Dik	Marian	Sander	Philip	Patrick	Frank						
Person Email	geo@ncbi.nlm.nih.gov												
Person Affiliation	UMC Utrecht												
Person Address	Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, Utrecht, Utrecht, Netherlands												
Person Roles	submitter												
Protocol Name	P-GSE42217-2	P-GSE42217-1	P-GSE42217-4	P-GSE42217-3	P-GSE42217-9	P-GSE42217-8	P-GSE42217-5	P-GSE42217-7	P-GSE42217-6	P-GSE42217-10	P-GSE42217-13	P-GSE42217-11	P-GSE42217-12
Protocol Description	ID_REF =  VALUE = -INV_VALUE: normalized log2 ratio Cy3/Cy5 test/ref) Signal Norm_Cy5 =  Signal Norm_Cy3 = 	ID_REF =  VALUE = normalized log2 ratio Cy3/Cy5 test/ref Signal Norm_Cy5 =  Signal Norm_Cy3 = 	ID_REF =  VALUE = normalized log2 ratio (Cy5/Cy3) Signal Norm_Cy5 =  Signal Norm_Cy3 = 	ID_REF =  VALUE = normalized log2 ratio (Cy3/Cy5) Signal Norm_Cy5 =  Signal Norm_Cy3 =  INV_VALUE = normalized log2 ratio (Cy5/Cy3)	scanning of slides using Agilent G256BA Imagene feature extraction	Tecan HS4800 hybridization	yeast RNA isolation for robotic amplification v1.0	yeast HTP RNA isolation for robot v2.0	robot amplification and labeling v1.0	Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.	Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.	yeast-deleteome[grow]	Yeast growth for expression profiling in Tecan platereader v1.0
Protocol Type	bioassay_data_transformation	bioassay_data_transformation	bioassay_data_transformation	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	nucleic_acid_extraction	labeling	feature_extraction	feature_extraction	grow	grow
Experimental Factor Name	GENETIC MODIFICATION	GENOTYPE											
Experimental Factor Type	genetic modification	genotype											
Comment[SecondaryAccession]	GSE42217												
Comment[GEOReleaseDate]	2012-11-14												
Comment[ArrayExpressSubmissionDate]	2012-11-09												
Comment[GEOLastUpdateDate]	2012-11-15												
Comment[AEExperimentType]	transcription profiling by array												
SDRF File	E-GEOD-42217.sdrf.txt