Total RNA was isolated using the peqGOLD Total RNA Kit (12-6834-02, Peqlab) together with the peqGOLD DNase I Digestion Kit (732-2982, Peqlab) and the integrity of RNA was evaluated on a 1.2% Agarose/TAE gel. For RT-qPCR cDNA was prepared from 1 μg of total RNA using the SensiFAST cDNA Synthesis Kit (BIO-65054, Bioline) and analysed by qPCR using the SensiFast SYBR Lo-ROX Kit (BIO-94050, Bioline) according to manufacturer’s instructions together with gene-specific primers (S4 Table). Amplification reactions were measured in triplicates on a Stratagene Mx3000P thermocycler (Agilent Technologies) and the mean values were calculated according to the ΔΔCt method using the mRNA levels of Rp49 as a normalisation reference. mRNA expression was calculated relative to samples treated with a non-targeting dsRNA against GFP. Error bars represent the standard deviation from five biological replicates.

For RNA sequencing the total RNA from three independent dsRNA transfections was isolated. The integrity of RNA was assessed on an Experion StdSens RNA Chip (Bio-Rad). RNA-seq libraries were prepared using a TruSeq Stranded mRNA Library Prep kit (Illumina). Libraries were quantified on a Bioanalyzer (Agilent Technologies) and sequenced on an Illumina HiSeq 1500 platform, rapid-run mode, single-read 50 bp (HiSeq SR Rapid Cluster Kit v2, HiSeq Rapid SBS Kit v2, 50 cycles) according to the manufacturer’s instructions.

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