Visualize Gene Expression and Splice Junctions at the Single-cell Level Using the RNAscope™ and BaseScope™ in situ Hybridization Assays

The nervous system consists of numerous specialized cell types that remain to be fully characterized at the molecular level. Due to the high degree of structural and functional heterogeneity and the intricate spatial organization of these cells, analysis of gene expression within the morphological and spatial tissue context is invaluable. The RNAscope™ in situ hybridization (ISH) assay enables highly sensitive and specific visualization of gene expression visualization within the nervous system. BaseScope™ is an ISH assay that allows visualization of splice junctions between adjacent exons and/or retained introns in order to characterize alternative splicing events in cells and tissues. This application note highlights case studies for both ISH assays in the nervous system:

• In situ detection of G protein-coupled receptors (GPCRs) in the adult mouse brain using the RNAscope ISH assay
• In situ detection and visualization of EGFRvIII splice variant in human glioblastoma using BaseScope ISH assay
• In situ detection of circular RNAs in the developing mouse brain using BaseScope ISH assay