Highly multiplexed spatial mapping of diverse gene signatures and cell type specific markers across mouse brain using the RNAscope™ HiPlexUp in situ hybridization assay

Transcriptomic studies have ushered into an era of single cell technologies that are crucial for both classifying and characterizing known and novel cell populations of complex heterogenous tissues. However, such techniques are limited using dissociated cells that result in the loss of spatial organization of these cell populations, thus requiring a highly multiplexed approach that can interrogate gene expression at a single cell resolution while retaining the morphological context.

• scRNA-seq is a powerful approach to cell type discovery and classification, however, the resulting cell types and markers require confirmation and mapping with spatial context.
• Multiplexed RNAscope ISH complements scRNA-seq experiments by putting scRNA-seq findings in tissue context at single-cell resolution and single-molecule sensitivity. 
• The new RNAscope HiPlex technology enables simultaneous visualization of up to 48 targets and multiple cell types and subtypes on the same tissue section, providing a powerful new tool for neuroscience and beyond.