Comment[ArrayExpressAccession] E-MEXP-2070 Investigation Title Transcription profiling by array of Drosophila head and thorax from females mated with sex peptide null or sex peptide producing males Comment[Submitted Name] Effect of Sex-Peptide transfer on gene and microRNA expression in Drosophila melanogaster mated females - gene profiling in Head-Thorax Publication Title Sex peptide of Drosophila melanogaster males is a global regulator of reproductive processes in females. Publication Author List Gioti A, Wigby S, Wertheim B, Schuster E, Martinez P, Pennington CJ, Partridge L, Chapman T Publication DOI 10.1098/rspb.2012.1634 PubMed ID 22977156 Experimental Design co-expression_design time_series_design individual_genetic_characteristics_design replicate_design transcription profiling by array Experimental Design Term Source REF MGED Ontology MGED Ontology MGED Ontology EFO Comment[AEExperimentType] transcription profiling by array Comment[MIAMExpressLogin] agioti Comment[MIAMExpressSubmissionID] 5502 Experiment Description Comparison of females mated to males null for Sex-Peptide (SP0, Liu, H. and E. Kubli, Sex-peptide is the molecular basis of the sperm effect in Drosophila melanogaster. Proc Natl Acad Sci U S A, 2003. 100(17): p. 9929-33) or to control, Sex-Peptide producing, males. Comparisons were made at 3 and 6 hours after mating, in dissected Head-Thorax body parts. Experimental Factor Name growth condition time Experimental Factor Type growth condition time Person Last Name Gioti Person First Name Anastasia Person Email a.gioti@ucl.ac.uk Person Phone 020 7679 4387 Person Fax Fax: 020 7679 7096 Person Affiliation UCL Person Address Biology, GEE, Gower Street, Darwin Building, London, London, WC1E 6BT, United Kingdom Person Roles submitter Person Roles Term Source REF MGED Ontology Quality Control Type biological_replicate Public Release Date 2009-08-01 Comment[ArrayExpressSubmissionDate] 2009-02-24 17:35 Protocol Name P-MTAB-3422 P-MTAB-3423 P-MEXP-7 P-MTAB-3425 P-MTAB-3426 Protocol Description Pairs of SP+ (wild-type) or SP0 (mutant) males, 5-6 days old, were aspirated into cryovials (180 vials in total). The next day, after lights-on, single 6-day-old virgin females were aspirated into each vial. Both males were removed from each vial after one mating occurred. Females that copulated for <10mins were excluded from further analysis. Females of each mating treatment (SP+ or SP0 males) that began copulating within 5 minutes of each other were formed into matched pairs for identical handling.

Collection of material (mated females) :

Females were snap-frozen at two time-points, 1) 180mins post-mating and 2) 360mins post-mating, and dissected into two body parts, 1) abdomen and 2) head-thorax.

Flies were reared and experiments performed on sugar-yeast food at 25C, in a non-humidified, 12-12hr light-dark room. Larvae were grown at standard density. Adult food was supplemented with excess live yeast.
(Parameters: time unit = seconds, min temperature = 25, temperature unit = C) Normalizations were performed using first GC-RMA (Wu, Z., et al., A Model Based Background Adjustement for Oligonucleotide Expression Arrays. Journal of the American Statistical Association, 2003. 99: p. 907-917) on all probes followed by

Loess (Yang, Y.H., et al., Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, 2002. 30(4): p. e15) on present probe sets (Schuster, E.F., et al., Correcting for sequence biases in present/absent calls. Genome Biol, 2007. 8: p. R125). The Cyber-T statistical analysis (Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: regularized t-test and

statistical inferences of gene changes. Bioinformatics 2001, 17:509-519) was used to perform a regularized paired t-test between genotypes for each time point. False discovery rates were estimated using the Storey method (Storey, J.D., The positive false discovery rate: a Bayesian interpretation and the q-value. Annals of Statistics, 2003. 31: p. 2013-2035). For the Head-Thorax dataset, normalizations and statistical analysis did not include the outlier sample SP null_3 hours_repl-e4. Total RNA was extracted using the mirVanaï¾™ kit (Ambion), following the manufacturer's protocol for total RNA isolation. Spin times were doubled to remove any excess reagents.


(Parameters: Extracted product = total_RNA, Amplification = none) The abdomen or head-thorax of females within each mating type (SP+ or SP0), each time point (180 or 360mins) and each biological replicate (4 in total) were combined into a single vial. Each pooled vial contained body parts from a mean of 67 flies.

Protocol Type specified_biomaterial_action grow bioassay_data_transformation nucleic_acid_extraction pool Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology Term Source Name MGED Ontology ArrayExpress EFO Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo SDRF File E-MEXP-2070.sdrf.txt