Fig. 1

Identification of poly(A) sites using 3′-tag-based scRNA-seq data. a The schematic diagram depicts the read distribution along the gene model for different scRNA-seq methods, including the tag-based methods, including STRT-seq and CEL-seq, and the full transcript method, such as Smart-seq2. b The plots depict the read coverage of poly(A) reads around poly(A) sites annotated in GENCODE, including canonical and variants, in different scRNA-seq datasets, including CEL-Seq2/A dataset, SCRB-seq/A dataset, and Microwell-seq dataset. The upper panels depict the average read coverage of poly(A) reads around poly(A) sites. Y-axis: the average read coverage; X-axis: the distance from upstream 100 nt to downstream 100 nt to annotated poly(A) sites. The lower panels show the read coverage for each poly(A) site using heatmaps. Additional examples are shown in Additional file 1: Fig. S1C-I. c–e Comparisons between identified poly(A) sites and annotated poly(A) sites. The Y-axis represents the count of poly(A) sites, and the X-axis represent the distance between the identified poly(A) sites and the closest annotated poly(A) sites, c is for CEL-seq2/A dataset, d is for SCRB-seq/A dataset, and e is for Microwell-seq dataset. Additional examples are shown in Additional file 1: Fig. S2B, C. f Canonical poly(A) motif (AAUAAA) enrichments for novel poly(A) sites identified using five different scRNA-seq datasets, including CEL-seq2/A, CEL-seq2/B, SCRB-seq/A, SCRB-seq/B, and Microwell-seq. P-values and percentage of targets are shown. g The line plots illustrate the canonical poly(A) signal (AAUAAA) distribution from upstream 50 nt to downstream 50 nt to novel poly(A) sites. Y-axis: the canonical poly(A) signal (AAUAAA) frequency; X-axis: the distance from upstream 50 nt to downstream 50 nt to novel poly(A) sites. h The IGV plot depicts the read distributions on human CCDC173 gene. The upper three tracks represent the bulk RNA-seq read distributions of Gm12878, HepG2, and HEK293 cell line. The bottom track represents pooled scRNA-seq read distributions of HEK293 cell line. The identified novel poly(A) site is marked by the dashed red line