PLP-seq: improving nanopore accuracy using splint mediated padlock probe ligation enables the sequencing of isoform and RNA editing in mouse brain

Spatial RNA sequencing (RNA-seq) has been applied to healthy and tumor tissue to quantify gene expression in situ. While high-throughput sequencing methods offer high accuracy, it provides limited information on splicing events. Here we compared five cDNA circularization methods in generating consensus reads from nanopore long-read sequencing, and present a novel method that integrates splint-mediated lock probe ligation (PLP), 10x Genomics Visium and nanopore sequencing methods, PLP-seq. Applying PLP-seq on mouse brain sections and an improved bioinformatic pipeline, we identified novel splicing junctions, RNA isoforms and RNA editing on showing distinct spatial patterns. PLP-seq offers spatial information on full-length RNA-seq, providing opportunities to analyze complex biological systems and tumor heterogeneity at the gene- and isoform-level.