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While spatial compartmentalization of gene expression has been mainly studied during development, increasing evidence shows that unique expression patterns are maintained throughout adulthood. Yet, considerably less known is known about how or why different cell populations maintain their distinct spatial organizations in adult tissues. Indeed, compartmentalization of gene expression is integral for defining the functional properties of tissues.

Freyberg and colleagues have employed multiplex fluorescent in situ hybridization (FISH) via RNAscope to dissect cell type-specific patterns of gene expression across three adult tissues: liver, pancreas, and brain. Importantly, the HALO® FISH module was used to quantitatively analyze cell-type-specific patterns of gene expression in two- and three-dimensions across different metabolic zones of liver, the striatal region of brain, and in pancreatic islets. In brain, the Spatial Analysis module generated heat maps of gene expression to identify the three-dimensional distributions of striatal cell subpopulations. In pancreatic islets, the Tissue Classifier module quantified anatomically-driven differences in the distributions of several cell types. Overall, using HALO to spatially resolve broader patterns of gene expression across different tissues has led to the discovery of new cell populations. The capabilities provided by these HALO modules has also created new links between spatial differences in gene expression and functionally distinct tissue regions to generate new biological insights for current projects.