STAR Protocols (Sep 2023)
Mapping alternative polyadenylation in human cells using direct RNA sequencing technology
Abstract
Summary: Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate mRNA isoforms with alternative 3′ untranslated regions. Here, we detail a protocol for detecting APA genome wide using direct RNA sequencing technology including computational analysis. We describe steps for RNA sample and library preparation, nanopore sequencing, and data analysis. Experiments and data analysis can be performed over a period of 6–8 days and require molecular biology and bioinformatics skills.For complete details on the use and execution of this protocol, please refer to Polenkowski et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.