NCM 2022: Single-cell transcript isoform sequencing of the activated adult mouse hippocampus with 10x Genomics and Oxford Nanopore

Using the rolling circle amplification to concatemeric consensus (R2C2) Nanopore error-correction protocol developed by Volden et al., we generated single-cell long-read transcriptomics data in the adult mouse hippocampus with 10x Chromium-generated cDNA. We are able to generate enough reads on the Oxford Nanopore PromethION device to successfully perform meaningful differential gene expression analysis for cell clustering and identification. The complete exon coverage generated by our single cell long reads allows for transcript isoform identification. We are applying this single cell isoform sequencing approach to the discovery of learning-specific transcript isoforms in a mouse model of contextual learning. The transcriptional response that cells of the brain undergo during activity begets mRNA regulation and synaptic protein function. We demonstrate, with Oxford Nanopore long-read sequencing, our ability to capture the diverse transcript isoform landscape of the activity induced transcriptional response with cell-type specificity.