Single-cell RNA editing profiling

Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) and Seurat (https://satijalab.org/seurat/) were applied to cluster and identify the cell types based on known marker expression. The marker genes were PRSS1, CTRB1, CTRB2, and REG1B for acinar cells, MS4A1, CD79A, CD79B, and CD52 for B cells, AMBP, CFTR, and MMP7 for type1 ductal cells, KRT19, KRT7, TSPAN8, and SLPI for type 2 ductal cells, CHGB, CHGA, INS, and IAPP for endocrine cells, CDH5, PLVAP, VWF, and CLDN5 for endothelial cells, LUM, DCN, and COL1A1 for fibroblast cells, AIF1, CD64, CD14, and CD68 for macrophage cells, ACTA2, PDGFRB, and ADIRF for stellate cells, and CD3E, CD4, and CD8 T cells (21 (link)). The reads for each cell type were extracted and combined. RNA editing events for each type were identified by REDItools. Then, credible RNA editing sites were filtered by satisfying stringent requirements (total reads for each site in each sample ≥10, 1 > editing level for each site in each sample ≥0.1, remove SNP sites).