Extended Data Fig. 4: Lineage decisions in the mammalian blastocyst.

Results from pooling cells of two replicates at E3.5 and E4.5, followed by Harmony augmentation. a, Force-directed layout of E3.5 and E4.5 cells depicting the relationship between three blastocyst lineages. Cells coloured by time point or annotated cell types. b, Plot showing projection of E3.5 and E4.5 cells along the first two diffusion components. Distances between lineages were computed using multiscale distances. c, Table showing the connectivity between different compartments in a kNN graph of E3.5 cells. Each row represents the fraction of outgoing edges from cells of the respective compartment that connect to cells in the compartments specified in the columns. d, Force-directed layout of E3.5 and E4.5 cells after removal of trophectoderm cells, showing relationships between ICM, EPI and PrE cells. Cells are coloured by time point or Phenograph¹⁴ clusters. e, Palantir^10,11 determined pseudo-time ordering, differentiation potential and branch probabilities of PrE and EPI cell lineages. f, Plots showing the second derivative of PrE and EPI differentiation potential along pseudo-time, which suggests that changes in differentiation potential—and therefore lineage commitment—in both lineages occur at E3.5. Points of highest changes along pseudo-time represent inferred lineage specification and commitment. g, Distribution of E3.5 lineage cells along pseudo-time. Each distribution represents cells from one Phenograph cluster. h, Histograms showing the distribution of differentiation potential (left), PrE fate probability (middle) and EPI fate probability (right) in the E3.5 ICM clusters. i, Gene expression patterns of parietal and visceral endoderm markers. Each cell is coloured on the basis of its MAGIC⁵⁰ imputed expression level for the indicated gene. Black and orange arrowheads mark presumptive parietal and visceral endoderm lineages, respectively.