J.M.Ranz, C.I.Castillo-Davis, C.D.Meiklejohn, D.L.Hartl, Sex-dependent gene expression and evolution of the Drosophila transcriptome, (Science 300: 1742-1745; 2003).
These experiments used arrays of full length cDNAs cloned and sequenced by the Berkeley Drosophila Genome Project and designated as DGC 1.0.
5928 cDNA clones were amplified by the polymerase chain reaction and analyzed by gel electrophoresis. These products were purified and spotted onto glass slides. In order to ensure quality, spots containing PCR products associated either with multiple bands, faint bands or with an unexpected size band were ignored. A total of 4776 clones were considered reliable.
For D. melanogaster, 4 replicate competitive hybridizations of male- vs. female-derived cDNA were performed. These included biological and dye-swap replicates. All hybridizations used 3-5 day old flies of the Canton-S strain.
For D. simulans, 5 replicate competitive hybridizations of male- and female-derived cDNA were performed. These included biological and dye-swap replicates. All hybridizations used 3-5 day old flies of the Sim-1 strain.
The ratios in Sebida are those given by the authors in the supplemental data accompanying the above publication. P-values were calculated from the raw data (kindly provided by J. Ranz) using a Bayesian method (BAGEL) developed by Jeffrey Townsend.