Incorporation of spatial mapping into single cell RNA sequencing workflow using a multiplex in situ hybridization technology - Presented at: 2020 AGBT Meeting

Complex and highly heterogenous tissues such as the brain are comprised of multiple cell types and states with exquisite spatial organization. Single-cell RNA sequencing (scRNA-seq) is now being widely used as a universal tool for classifying and characterizing known and novel cell populations within these heterogenous tissues, ushering in a new era of single cell biology. However, the use of scRNA-seq presents some limitations due to the use of dissociated cells which results in the loss of spatial context of the cell populations being analyzed. Incorporating a multiplexed spatial approach that can interrogate gene expression with single cell resolution in the tissue context is a powerful addition to the scRNA-seq workflow. In this study, we used the RNAscope Multiplex Fluorescent and RNAscope HiPlex in situ hybridization (ISH) assays to confirm and spatially map the diverse striatal neurons that have been previously identified by scRNA-seq in the mouse brain (Gokce et al, Cell Rep, 16(4):1126-1137, 2016).