Evaluating the potential and limitations of nanopore adaptive sampling for targeted transcriptome sequencing

Long-read RNA sequencing is a powerful technology for transcriptomics, but low throughput and high cost pose challenges. Adaptive sampling, a feature of Oxford Nanopore Technologies, offers real-time enrichment by selectively ejecting non-target molecules. We evaluate adaptive sampling for human transcriptome analysis. 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 SH-SY5Y human neuroblastoma cells, BT549 human breast cancer cells, and T47D human breast cancer cells.