RNA-seq.

Experimental details including sample collection, analysis parameters, and mapping efficiency are reported. Counts per million are reported for all mapped genes for each biological replicate in all experimental conditions. Fold changes, counts per million, p-values and false discovery rates are reported from the output of a generalized linear model. Fold changes, counts per million, p-values and false discovery rates are also reported from the output of an exact test for all comparisons between Hh-related gene RNAi-treated larvae and negative controls recovered on empty vector RNAi. Additionally, an exact test was performed pooling all biological replicates from the four Hh-related RNAi conditions and fold changes, counts per million, p-values and false discovery rates are reported. Finally, the complete gene enrichment output for all differentially expressed genes identified from the exact test on pooling all Hh-related RNAi treatment conditions from WormCat is provided. (XLSX)