RNA-seq analysis to assess transcriptional effects of Rp mutations in wing imaginal discs and their dependence on Xrp1

Since the putative transcription factor Xrp1 gene is required for many aspects of Rp+/- phenotypes, we sought to define what transcriptional changes occur in Rp+/- wing discs and their dependence on Xrp1. We identified 257 genes whose transcripts were significantly altered in the same direction in two Rp+/- genotypes, most of which depended on Xrp1. The results show that Xrp1 regulates a significant transcriptional response in Rp+/- genotypes. Overall design: 12 samples with wildtype (named as frt82_w) in triplicate, one type of Rp+/- (named as M67_w) in triplicate, and the other type of Rp+/- (named as M95_w) in triplicate, as well as RpS3+/- Xrp1+/- (named as M2-73_M95) in triplicate