Genome-wide differences in RNA expression in Drosophila melanogaster leg imaginal discs based on time and presence/absence of broad-based gene regulation

We report on changes in gene expression resulting from the ecdysone-directed broad-based transcriptional regulatory hierarchy in Drosophila melanogaster leg imaginal discs by comparing expression in white1118 third-instar larvae (-18 hrs relative to pupariation) and white prepupae (0 hrs) to examine the transcriptional effects of the late larval ecdysone pulse, as well comparing expression in white1118 and broad5 white prepupal leg imaginal discs to examine the transcriptional effects of the early ecdysone responder, broad. Using this approach, we were able to identify critical leg disc elongation genes that are differentially regulated in broad mutants RNA sequencing of leg imaginal discs in white1118 larvae/prepupae at -18 hrs and 0 hrs and in broad5 prepupae at 0 hrs. Each genotype/timepoint combination was sequenced in triplicate.