RNAscope technology enables the incorporation of spatial mapping and confirmation of gene signatures into single cell RNA sequencing workflows

In this application note, the diverse cell types in the mouse striatum that have been previously identified by scRNA-seq were confirmed and spatially mapped using the RNAscope^TM Multiplex Fluorescent assay and the RNAscope^TM HiPlex assay. The major and minor gene signatures identified by scRNA-seq, including discrete D1 and D2 medium spiny neuron (MSN) subtypes, were confirmed.

Further cellular heterogeneity within the MSN subpopulations was marked by a transcriptional gradient, which was spatially resolved with the RNAscope^TM technology.