Fig. 4

Using quantified PASs to represent distinct transcript expression for refining cell identities. a Schematic of single-cell analyses with either differential gene expression (DGE) or differential transcript expression (DTE) with SCAPTURE-identified and SCAPTURE-quantified PASs. b Numbers of expressed transcripts per gene in combined six PBMC datasets from 10x Genomics. c Number of expressed genes or transcripts in combined six PBMC datasets from 10x Genomics. d Gene distribution of top 2000 highly variable PAS-based transcript features. Of note, the majority of these top variable features are associated with genes expressing APA transcripts. e Phylogenetic analysis of cell types clustered by DTE with SCAPTURE (left) or by DGE with the conventional Seurat protocol [31] (right). f Cross comparison of cell types assigned by DTE or DGE. g Comparison of marker gene expression between DGE-assigned major cell types (black) and DGE-unassigned but DTE-assigned cells (red). Of note, among the DGE-unassigned but DTE-assigned cells, some showed similar marker gene expression patterns as natural killer cells (NKCs; 68 out of 237) or dendritic cells (DCs; 48 out of 237). h Phylogenetic re-analysis of cell types clustered by DTE (left) or by DGE (right). DGE-unassigned but DTE-assigned cells are highlighted in both clusters (red)