Megan L. Noonan from Washington University School of Medicine in St. Louis spoke at the Nanopore Community Meeting in Boston. The session’s title was “Bulk and single-cell nanopore transcriptomics to identify alternative splicing in renal tubule cells.” Noonan spoke about the need to create new therapeutics for therapeutics. They explained that alternative is a regulatory mechanism. Short-read sequencing allows for more accurate quantification and isoform discovery. Noonan explained that SRSF-7 knockdown experiments and nanopore reads can help identify isoforms and expression patterns. Noonan used the Bambu package to analyze RNA seq data. They also used the 10X Genomics platform and ONT workflow for single-cell transcriptomics in mouse kidneys. Noonan explained that with long-read single-cell transcriptomics, they uncovered unique clustering. Noonan also performed differential transcript usage (DTU) between cell types. They used the DTurtle package that identified the ten most significant DTU genes. Interestingly, the functional consequences of one isoform switching affect perm selectivity! Noonan showed that loss of SRSF-7 in tubule cells upregulated inflammatory pathways and decreased cell proliferation. Single-cell nanopore sequencing showed “split” cell type clusters, and bulk nanopore sequencing of transcripts allowed the discovery of DTU not found with short reads. While I don’t understand all the transcriptomics details, I appreciate the variety of tools used!
