RNA-seq following knockdown of a sex determing gene in house fly

We injected double-stranded RNA (dsRNA) into house fly embryos to knock down transformer (Md-tra), creating sex-reversed males that do not carry a Y chromosome. We also injected dsRNA trageting GFP as a sham treatment. We used RNA-seq to compare gene expression in the sex-reversed males with genotypic (normal) females (injected with dsRNA targeting GFP) and two types of genotypic (normal) males (injected with dsRNA targeting Md-tra or GFP). The expression profiles of sex-reversed males were similar to normal males. In contrast, about two thousand genes are differentially expressed between sex-reversed males and normal females, a similar magnitude as between normal males and females. Overall design: Four different genotype by treatment combinations were assayed: 1. genotypic males treated with dsRNA targeting Md-tra; 2. genotypic males treated with dsRNA targeting GFP; 3. genotypic females treated with dsRNA targeting Md-tra (sex-reversed males); 4. genotypic females with dsRNA targeting GFP. For each genotype by treatment combination, expression was measured in both head and abdomen. Three biological replicates of each genotype by treatment and tissue were assayed.