Fig. 2

Identification of differentially expressed neuronal transcripts in response to RNAi-mediated silencing of Caz, Smn or TBPH in adult flies. A Schematic representation of the experimental set-up for RNA-seq analysis. Hormone-dependent, adult-onset expression of short hairpin (sh) RNA was used to induce RNAi-mediated gene silencing of caz, Smn or TBPH. RNA was prepared from fly heads five to seven days post induction of shRNA expression, quality checked and subjected to mRNA-seq. Fly lines with shRNA against the always early (ae) embryonic gene served as control. B Bar graph showing the RNA-seq log2 fold change of the siRNA target genes plus the Gapdh housekeeping gene in each RNAi fly line. Statistically significant differences to the ae siRNA fly line are indicated as ** (adjusted p value < 0.05) and * (adjusted p value = 0.06 and p value < 0.02). C Bar graph showing the number of upregulated (red), downregulated (green) and differentially spliced mRNAs (yellow) in each RNA-seq dataset. Note that the kind of splicing change was not considered for this analysis. D Venn diagrams and corresponding bar graphs showing the overlap in upregulated (top), downregulated (middle) or differentially spliced (bottom) mRNAs in flies with RNAi-mediated silencing of caz, Smn or TBPH. The bar color compares the expected (black) and observed (red) overlap given the total transcripts altered in response to the silencing of caz, Smn or TBPH, respectively. The size of randomly expected overlaps and the statistical tests comparing observed with expected overlaps were calculated using the SuperExactTest R package. All shown overlaps are significantly larger than expected by chance (observed and expected overlap sizes and respective p-values are presented in Supplementary data file 5