A triplicate of RNA samples from lin-52 mutant and WT L1 worms were rRNA-depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina, 20037135) and sequenced using a Hiseq4000 (Illumina) with PE75 read length. For RNA quality control, the RNA integrity number was ≥9.4 for all samples. RNA-seq data were processed through the QuickNGS pipeline83 (link), Ensembl version 85. Reads were mapped to the C. elegans genome using Tophat84 (link) (version 2.0.10) and abundance estimation was done using with Cufflinks85 (link) (Version 2.1.1). DESeq2 (ref. 76 (link)) was used for differential gene expression analysis.
The human RNA-seq data were processed with Salmon-1.1 (ref. 86 (link)) against a decoy-aware transcriptome (gencode.v37 transcripts and the GRCh38.primary_assembly genome) with the following parameters: –validateMappings –gcBias –seqBias. The output was imported and summarized to the gene-level with tximport (1.14.2)87 (link), and differential gene analysis was done with edgeR (3.28.1)88 (link).
The human RNA-seq data were processed with Salmon-1.1 (ref. 86 (link)) against a decoy-aware transcriptome (gencode.v37 transcripts and the GRCh38.primary_assembly genome) with the following parameters: –validateMappings –gcBias –seqBias. The output was imported and summarized to the gene-level with tximport (1.14.2)87 (link), and differential gene analysis was done with edgeR (3.28.1)88 (link).
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