Tonight I watched Sheridan Cavalier from The John Hopkins University School of Medicine present at the Nanopore Community Meeting 2022. The title of the session was “Single-cell transcript isoform sequencing of the activated adult mouse hippocampus with 10x Genomics and Oxford Nanopore.” Cavalier is a graduate student and developed an approach to sequence mouse hippocampus cells. Cavalier explained the concept of activity-induced transcription that is required for learning and memory consolidation. They explained that activity-induced transcription is known to involve thousands of genes, is cell-type specific, and involves alternative splicing. Cavalier noted that activity-induced transcription presents a diversity of transcript isoforms. They generated a dataset from single-cell isoform sequencing with 10X Genomics and Oxford Nanopore. They explained that the canonical 10X pipeline is limited to gene-level and short read sequencing. Cavalier used the R2C2 approach in which DNAs are circularized and sequenced. They sequenced on both Nanopore and an Illumina MiSeq. They concluded that they get the same quality with 10x the read length. Cavalier used a classical conditional experiment and was able to identify and quantify with Minimap2 and Salmon Quant… at the isoform level! Cavalier’s goal is to isolate learning-specific isoforms with this approach. I am left thinking about the applications of this approach: there are so many possibilities!
