Gene-expression changes due to an altered gene dose on autosomes. (a) Experimental design to measure gene-expression changes for altered autosomal gene dose. Replicate mRNA samples from flies bearing a duplication, Dp(2;2)Cam3/+, or a deletion, Df(2L)JH/+, on the left arm of autosomal chromosome 2 (2L) were labeled with either Cy3 or Cy5 and hybridized to FlyGEM arrays. These were performed as dye-swap experiments to avoid any effect of dye bias. Following data extraction, changes in expression ratios as a result of differences in the dose of individual genes were determined. There are no differences in underlying gene dose outside the region of the aberrations, and there is a 1.5-fold difference when a gene is present on the duplication (Dp) or a 3-fold difference when the gene is present on the duplication and deleted in the deficiency (Df). (b) Average expression ratios from duplicate experiments comparing Dp/+ vs Df/+ adult male flies were plotted as a moving average against gene position along 2L. Gene-expression ratios for no gene dose difference (black), 1.5-fold (green) and 3-fold (orange) gene doses are indicated. Breaks in gene-expression ratios occur at the predicted cytological breakpoints of the aberrations. The aberrations are cartooned below the moving average plot, with the Dp (triangle) and Df (gap) indicated. In addition, the diploid regions of the genome where Dp/+ flies show greater expression than Df/+ flies are indicated (arrow).