Characterizing the transcriptomic profiles of individual cells by single-cell RNA sequencing (scRNA-seq) has become a universal tool to identify both known and novel cell populations and to understand tissue structure and function. However, scRNA-seq uses dissociated cells and results in the loss of spatial organization of the cell population being analyzed.
This application note explains how confirmation and spatial mapping of scRNA-seq results can be obtained using assays that retain spatial organization, such as RNA in situ hybridization. In particular, it demonstrates the use of ACD’s RNAscope Multiplex Fluorescent and HiPlex assays for the confirmation and spatial mapping of scRNA-seq results in the highly complex and heterogenous mouse striatum.
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