TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing

Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings. Overall design: Targeted long-read sequencing on the Oxford nanopore platform was used to profile full-length transcript isoforms of preselected genes in poly(A)-selected RNA from human brain tissue (Clontech) and SH-SY5Y human neuroblastoma cells, each with three replicates. Targeted long-read sequencing was also used to examine full-length transcript isoforms of 468 actionable cancer genes in poly(A)-selected RNA extracted from 40 breast cancer cell lines (ATCC).