A single-embryo, single-cell time-resolved model for mouse gastrulation

Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here, we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 h of molecular diversification. Using algorithms and precise timing, we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multifurcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition. [Display omitted] •Single-embryo scRNA-seq synthesis of morphology and transcriptional staging•A network flow model infers differentiation of embryonic cell ensembles•Gastrulation is dominated by progenitor states that continuously multi-furcate•Single-embryo chimeras control functional studies of TFs over time and lineage A time-resolved, high-resolution model charts differentiation dynamics during mouse gastrulation and reveals that for most lineages, cell fates arise from multi-furcation events rather than classical tree-like bifurcation.