The emergent landscape of the mouse gut endoderm at single-cell resolution

To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. We uncover an unappreciated relationship between descendants of these lineages, before the onset of gastrulation, suggesting that mixing of extra-embryonic and embryonic endoderm cells occurs more than once during mammalian development. We map the trajectories of endoderm cells as they acquire embryonic versus extra-embryonic fates, and their spatial convergence within the gut endoderm; revealing them to be globally similar but retaining aspects of their lineage history. We observe the regionalized localization of cells along the forming gut tube, reflecting their extra-embryonic or embryonic origin, and their coordinate patterning into organ-specific territories along the anterior-posterior axis. Cells were isolated from sequentially-staged wild-type mouse embryos between E3.5 and E8.75. Whole embryos were used for single-cell isolations for stages E3.5-E5.5. Endodermal tissue layers were isolated from E6.5-E8.75 stages. Gut tube of E8.75 were sorted based on GFP expression and another dataset was generated using anterior - posterior positioning. Each sample was measured in replicate with E5.5 and E7.5 measured in triplicates.