Extended Data Fig. 5: Gene expression trends in EPI, PrE, visceral and parietal endoderm lineages in the blastocyst.

a, Plots comparing gene expression trends along pseudo-time for genes that encode components of the FGF signalling pathway (Fgf4, Fgf5, Fgf8, Fgfr1, Fgfr2 and Spry4), the endoderm-marker transcription factors Gata6, Gata4, Sox7 and Sox17, and Nanog during EPI and PrE lineage specification. Solid line represents the mean expression trend and shaded region represents ± 1 s.d. b, Dynamics of transcription factor ratios as lineages emerge. Ratio between Gata6 and Nanog, and Gata6 and Fgf4 along EPI; and between Nanog and Gata6, and Fgf4 and Gata6 along PrE, compared to changes in differentiation potential (dotted line). Transcription factor ratios were computed for each cell by using the MAGIC⁵⁰ imputed data for each gene. c, Plots comparing gene expression trends along pseudo-time. Gata and Sox transcription factors, Fgf receptors or Fgf ligands during PrE or EPI specification. Colours at the bottom of each panel represent time point and—where applicable—E3.5 and E4.5 Phenograph clusters. Dashed lines represent branch probabilities in commitment towards respective lineages. d, Gene expression patterns of FGF signalling pathway components, and Gata and Sox transcription factor genes. Orange, black and green arrowheads point to high expression in parietal endoderm, visceral endoderm and EPI, respectively. e, Laser-scanning confocal data depicting TCF7L1 expression at E3.5 (top panel) (n = 14) and E4.5 (bottom panel) (n = 11). SOX2 and GATA6 were used as EPI and PrE lineage markers, respectively. f, Gene expression patterns of Tcf7l1 and Nanog depicting similar expression of Tcf7l1 in EPI as Fgf4 (green arrowhead).