Population transcriptomics of Drosophila melanogaster females

To investigate the effect of sex on within- and between-population variation in gene expression, we performed a microarray analysis of adult females from 16 strains of Drosophila melanogaster, including eight strains from the putative ancestral range in sub-Saharan Africa and eight strains from a European population. The results were compared to those of a previous study of adult male gene expression variation among the same strains (GSE8843). We used dual-channel microarrays to compare genome-wide expression profiles in adult females from 16 inbred strains derived from two natural populations. In total, 56 hybridizations were performed including dye-swaps. The hybridization scheme consisted of a balanced loop design, which allowed an unbiased comparison of relative expression levels within and between populations.