RNA-Seq of whole Drosophila larval central nervous systems (mid-3rd instar stage, central brain + ventral nerve cord) with panneuronal ISWI knockdown and controls

Sleep disruptions are among the most commonly-reported symptoms across neurodevelopmental disorders (NDDs), but mechanisms linking brain development to normal sleep are largely unknown. From a Drosophila screen of human NDD-associated risk genes, we identified the chromatin remodeler Imitation SWItch/SNF (ISWI) to be required for adult fly sleep. To better understand the mechanisms by which ISWI regulates sleep, we performed RNA-Seq analysis on mid-3rd instar larval central nervous systems (central brain + ventral nerve cord) in the setting of pan-neuronal ISWI knockdown (elav-GAL4>UAS-ISWI RNAi) compared to controls (elav-GAL4;+). We chose mid-3rd instar because temporal mapping revealed ISWI knockdown during this pre-adult developmental stage led to adult fly sleep deficits. Overall design: Experimental: elav-GAL4>UAS-ISWI RNAi (4 replicates) versus controls: elav-GAL4; + (3 replicates). All samples were from 4 days post-egg lay (the mid-3rd instar larval stage), with at least 40 CNS per replicate.