In Situ Imaging of mRNA Splicing Variants by SpliceRCA

We present a method for multiplexed in situ imaging of individual RNA splicing variants. This method enables quantifying RNA splicing variants with single-molecule resolution, discriminating splicing isoforms with single-base precision as well as analyzing the subcellular localization of transcripts. With this technology, it is possible to study cell heterogeneity of gene expression, potentially helping to decipher rich diversity in posttranscriptional function and assist clinical monitoring.