Study Nocte's functions in transcription and translation in Drosophila eye discs

Nocte is an RNA binding protein but its functions in Drosophila eye development is unknown. We found that knockdown of nocte by RNAi in Drosophila eyes leads to small and rough eye phenotypes. We detected nocte's functions at mRNA levels by doing RNA-seq with purified polyA mRNA. We detected nocte's functions in mRNA translation by doing Ribo-seq and total RNA-seq to calculate the translation efficiencies. Overall design: For polyA RNA-seq, 20 pairs of late L3 eye discs were used in one repeat, and three repeats for WT and ey>nocte-RNAi eye discs were done. For Ribo-seq, 50 pairs of late L3 eye discs were used in one repeat, and three repeats for WT and ey>nocte-RNAi eye discs were done. The total RNAs from two repeats of WT and ey>nocte-RNAi samples for Ribo-seq were used for total RNA-seq. The samples in total RNA-seq were treated with rRNA depletion and submitted for RNA-seq.