Comment[ArrayExpressAccession] E-GEOD-52076 MAGE-TAB Version 1.1 Public Release Date 2013-11-06 Investigation Title eQTL Mapping of the Drosophila Female Head Transcriptome Comment[Submitted Name] eQTL Mapping of the Drosophila Female Head Transcriptome Experiment Description A dataset of ~600 RIL crosses using RILs from the Drosophila Synthetic Population Resource to be used for genomewide eQTL mapping. All samples are from female heads. 54 arrays with 12 samples per array resulting in data for 596 RIL crosses. 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 King King Long Macdonald Person First Name Elizabeth Elizabeth Anthony Stuart Person Mid Initials G G D J Person Email kingeg@missouri.edu Person Affiliation University of Missouri Person Address Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, MO, USA Person Roles submitter Protocol Name P-GSE52076-1 P-GSE52076-4 P-GSE52076-5 P-GSE52076-2 P-GSE52076-3 P-GSE52076-6 Protocol Description We performed standard quantile normalization and corrected for background effects using the normalize and backgroundCorrect functions in the oligo package in R We created a custom probe-to-transcript map using the most recent version of the CDS file available at FlyBase (v. 5.48) We identified probes containing SNPs in the DSPR RIL panel and eliminated any probes where the SNP had a significant effect We eliminated genes with fewer than 4 probes associated with it. We performed standard RMA using the basicRMA function in the oligo package to combine probe-specific data and generate a single expression measure per transcript We performed a principal components analysis and corrected all expression measures for the first 10 principal components to minimize batch effects We dropped any expression measures below background levels. ID_REF = VALUE = A normalized expression measure following RMA and correction for batch effects Labeling was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com. Hybridization was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com. Progeny from each cross were 3 -5 days old and raised on standard media in standard conditions. RNA was isolated using TRIzol Reagent (Life Technologies) and cleaned up using RNeasy Mini spin columns (Qiagen). Scanning was performed by the Carver Center for Genomics Microarray Center at the University of Iowa, following their standard operating protocol. See www.nimblegen.com. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name MATERNAL RIL PATERNAL RIL Experimental Factor Type maternal ril paternal ril Comment[SecondaryAccession] GSE52076 Comment[GEOReleaseDate] 2013-11-06 Comment[ArrayExpressSubmissionDate] 2013-11-04 Comment[GEOLastUpdateDate] 2013-11-06 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-52076.sdrf.txt