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Mammalian tissues are often composed of repeating anatomical units that are polarised by morphogens or directional blood flow. Thus single cells at different tissue coordinates operate in distinct microenvironment.
This spatial diversity enables optimisation of tissue function by allocating different tasks to cells that reside in distinct tissue locations. To explore this spatial division of labor on a genome-wide scale we are combining single cell transcriptomics with in-situ measurements in intact tissues to enable inference of the sequenced cells’ original tissue locations. This approach enables reconstructing global spatial gene expression atlases. I will demonstrate these approaches on two stereotypical and highly structured organs - the liver and the intestinal epithelium.