CryEx.v2, an enhanced protocol for the quantitative detection and visualization of cryptic splicing using human transcriptome data

Unraveling the mechanisms that suppress cryptic splicing is essential for maintaining transcriptome stability and developing therapeutic strategies in genetic disorders such as cancer. Here, we present a protocol to identify cryptic exons in human epithelial breast cells and quantify their inclusion utilizing RNA sequencing (RNA-seq) data. We describe steps for determining precise chromosome coordinates, calculating percent-spliced-in (PSI) values, classifying exons based on isoform presence, and conducting differential splicing analysis across conditions. We also detail procedures for visualizing a representative splicing event. For complete details on the use and execution of the original and this updated protocol, please refer to Zheng et al. 1 1. Zheng, R. ∙ Dunlap, M. ∙ Bobkov, G.O.M. ... hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing Mol. Cell. 2024; 84 :2087-2103.