Whole-transcriptome-scale isoform-resolved spatial imaging of single cells in tissues

Here, we introduce an in situ RNA amplification method and its integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to detect short RNA sequences and enable isoform-resolved spatial transcriptomics of individual cells in intact tissues.

Using this approach, we imaged ~33,000 distinct RNAs—including ~23,000 genes and ~10,000 isoforms—in the mouse brain. Our data enabled systematic analyses of region- and cell-type-specific gene programs and ligand-receptor-based cell-cell communications. These data further revealed rich spatial diversity and cell-type specificity in isoform usage across numerous genes, as well as brain structures particularly rich in specific isoform usage.