Fig. 2: Development of WPS and data quality control.

a Comparison of the C. elegans transcriptome across developmental stages. The Pearson correlation coefficient (PCC) was calculated by the WPS profiles of animals fed vector control bacteria and collected at different time points post L1. b Subsampling analysis of WPS profiles, combining data from 62 to 65 h for each replicate shown in Fig. 2a. The plot shows the fraction of genes quantified versus sequencing depth. Genes whose expression levels in subsampling fall within roughly ±30% interval of the reference value were considered as quantified (for detailed definition, see Supplementary Methods). Error bar shows the mean values (± s.d.) from three replicates of the subsampling profile. c Representative Principal Component Analysis (PCA) results for gene expression profiles of perturbations without (gna-1 on top panel) and with (iars-2 in bottom panel) a low-quality outlier replicate. Red and gray dots indicate RNAi and control samples, respectively. d An example showing reads mapped to the reverse strand of the RNAi target gene (nhr-7) and a decrease in mRNA reads at the 3’ end. The reads mapped to nhr-7 gene locus were visualized by Integrative Genomics Viewer (IGV⁸⁹). nhr-7 RNAi was compared to vector control RNAi and another RNAi condition (nhr-14). Quantification of anti-sense RNA reads in a Sanger-sequenced (e) and an unvalidated (f) WPS sequencing library. Row names represent the intended RNAi gene (three replicates each) and column names represent the actual knocked down genes. Row names in red indicate wrong RNAi clones. Values are the log2(Count-Per-Million (CPM) + 0.01) of the reads mapped to the reverse strand of each gene in the columns. g Log2(Fold Change (FC)) of the RNAi targeted gene expression for the WPS sequencing library shown in (f). Pound key (#) indicates not detected. Each bar represents the mean (±s.d.) and each dot represents one biological replicate (n = 3). Source data are provided as a Source Data file.