Fig. 6.

The comparison of cell states and germ layer identities between gastruloids and the early mouse embryo highlights differences in developmentally early populations. (A) UMAP plots displaying MNN-based integration of a comprehensive mouse sc-atlas (Pijuan-Sala et al., 2019) from E6.5 to E8.5 with the gastruloid datasets of 24, 48 and 72 hpa. Cell types were labelled according to germ layer identity or differentiation state to identify convergent populations. There is substantial overlap of mesodermal II and III, and endodermal gastruloid clusters to cells from the native embryo, but little intersection of less differentiated and neural or neuroectodermal populations with corresponding mouse cell types. (B) UMAPs are plotted as above; however, gastruloid cells are filtered by developmental day instead of germ layer identity. (C) Expression of marker genes for pluripotency, cell adhesion, EMT and mesodermal state, as well as general early differentiation compared between mouse epiblast and corresponding gastruloid populations (primed pluripotent, and early differentiated I and II).