Fig. 2: Identification of novel transcripts and isoforms in single cells.

a The number of transcripts with both ends captured using scRCAT-seq (n = 34), Smart-seq2 (n = 12), or ScISOr-seq (n = 8), versus cost. Shown is the mean number of transcripts shaded by 95% confidence intervals. b Comparison between scRCAT-seq (n = 10) and Smart-seq2 (n = 10) in terms of the ratio of reads covering the 5′ end of transcripts (5-bp range to the end). Significance was computed using two-sided Wilcoxon test. The boxplot shows the median as center line, the interquartile range (IQR) as a box, the whiskers indicate 1.5 × IQR and the outliers as points. c The cost of scRCAT-seq (n = 18) and ScISOr-seq (n = 8) for detection of 1000 transcripts. Significance was computed using two-sided Wilcoxon test. The boxplot shows the median as center line, the interquartile range (IQR) as a box, the whiskers indicate 1.5 × IQR and the outliers as points. d Violin plots comparing the expression level between genes detected by scRCAT-seq (n = 3) and ScISOr-seq (n = 3). Gene expression levels were quantified by Smart-seq2 RPM value. Significance was computed using two-sided Wilcoxon test. e Barplot showing the number of novel isoforms of annotated genes and novel, unannotated transcripts in mouse oocytes. The number of transcripts for each category is indicated above the box. Error bars represent standard deviation of the mean (n = 3). f Barplot showing the number of novel isoforms of annotated genes and novel, unannotated transcripts in mouse DRG. Error bars represent standard deviation of the mean (n = 3). g Venn diagram for novel transcripts detected concordantly by scRCAT-seq, Smart-seq2, and ScISOr-seq. h Genome browser track for an example of a novel gene with alternative polyadenylation sites on a different exon. i Gel image showing validation result of novel gene in (h). Experiments were repeated three times with similar results. Source data are provided as a Source Data file.