Validating scRNAseq Data from Human Fetal Brain Using Automated, Highly Multiplexed in situ mRNA Detection with Single-cell and Single-transcript Resolution

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Single-cell RNA sequencing (scRNA-seq) has fundamentally expanded our understanding of tissue composition and heterogeneity. While this methodology enables unbiased and comprehensive identification of distinct cell types based on their transcriptomic profiles, it does not provide positional context in the tissue architecture, which is critical for understanding the interactions between cells and their native tissue microenvironment. Spatial validation of scRNA-seq data using in situ techniques enables investigation of tissue-specific expression patterns. A panel of genes identified by single-cell transcriptomics was selected according to their specificity and expression level in order to map all major cell types and most cell subtypes. The results enabled validation of functionally distinct cell populations identified by scRNA-seq and further elucidate the spatial distribution of developmental gene expression programs at the single cell level.