Reads were aligned to the C. elegans genome ce11 (Ensembl WBcel235.87) by HISAT2 (version 2.0.5) with default parameters. Aligned reads were assembled to transcripts and levels of these transcripts were quantified by using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/). FPKM (fragments per kilobase of transcript per million mapped reads) values were calculated by using RNA-seq. Quantitation pipeline and P values were calculated using EdgeR. Protein-coding genes whose FPKM values in wild type treated with control RNAi were greater than 1 were used for DEG analysis. Overlapping genes between our mRNA-seq data and published transcriptome data were analyzed by using WormExp (version 1.0). Venn diagrams were made by using Venn Diagram Plotter (http://omics.pnl.gov/software/venn-diagram-plotter), and representation factors for overlaps between two different gene sets were calculated (http://nemates.org/MA/progs/overlap_stats.html).

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