Single-cell transcriptomics reveals gene expression heterogeneity that is masked in bulk measurements. Long-read, isoform-resolved single-cell sequencing (e.g., nanopore sequencing of single-cell libraries) enables detection of cell-type-specific splicing and transcript isoforms that are difficult to resolve with short-read single-cell RNA-seq. This makes it possible to study processes such as isoform switching during development and differentiation.

For example, Lebrigand et al. showed that the mouse brain gene Clathrin light chain A (Clta) undergoes isoform switching during neuronal maturation, and identified 76 genes with cell-type-specific transcript usage.