Extended Data Fig. 6: Additional single-cell RNA-seq analyses of human blastoids.

a, Correlation analysis of blastoid clusters with cells from in vivo cynomolgus monkey embryos (gast, gastrulating cells; postE-EPI, post-implantation early epiblast; postL-EPI, post-implantation late epiblast; post-paTE, post-implantation parietal trophectoderm; pre-EPI, pre-implantation epiblast; preE-TE, pre-implantation early trophectoderm; preL-TE, pre-implantation late trophoectoderm). b, Single-cell RNA-seq was performed at days 3, 6 and 9 during blastoid derivation (n = 3). t-SNE plot of sequenced cells, coloured by cluster assignment. c, Quantification of the cellular composition of clusters in b. d, Expression of lineage markers from the t-SNE analysis in b. e, Pseudotime trajectories for the ELCs across a time course of blastoid derivation. Epiblast cells from human pre-implantation embryos are included as a reference. Plots show pseudotime (top), sample time point (middle) and cell identity (bottom). The variability of U6 cells across time points may be due to cellular heterogeneity and unsynchronized differentiation of naive human PSCs during blastoid formation. f, g, Pseudotime-dependent gene expression signatures for the ELCs. This analysis only includes epiblast-specific genes defined in Zhou et al.³¹. h, Representative immunofluorescence and phase-contrast images showing the expression of CCR7 in a human blastoid. Images are representative of at least three independent experiments. Scale bar, 100 μm. i, t-SNE plot from Fig. 2h, without velocity analysis.