RNA-Seq of whole Drosophila brains (mid-pupal stage) with panneuronal pdm3 knockdown and controls

Through an RNAi-based screen, we identified a gene, pdm3, required for sleep maturation in Drosophila. Pdm3, a transcription factor, coordinates an early developmental program that prepares the brain to later execute high levels of juvenile adult sleep. Through temporal mapping, we found that pdm3 acts during the mid-pupal stage of Drosophila development to control sleep ontogeny. As such, we profiled RNA expression in whole brains at this stage of development to identify possible downstream transcriptional changes in the setting of panneuronal pdm3 knockdown (Elav-GAL4> UAS pdm3 RNAi) and controls (Elav-GAL4 / +). Overall design: Experimental: Elav-GAL4 > UAS pdm3 RNAi (4 replicates) versus controls: Elav-GAL4 / + (4 replicates). All samples were from the mid-pupal stage, defined visually as brown pupae (~6 days post-egg lay at 25c)