Extended Data Fig. 1: Quality control of scRNA-seq dataset.

a, Dorsal view of the dissected embryonic disk showing the primitive streak and node (Scale bar = 500μm; n = 1). b, Brightfield images showing embryo dissection with schematic diagrams highlighting the three anatomical regions collected (yolk sac, rostral and caudal regions of embryonic disk; Scale bar = 500μm; n = 1). c, Metrics used to assess the quality of the scRNA-seq libraries. From top to bottom the scatter plots show the number of detected genes, the fraction of reads mapped to the human genome, the fraction of reads mapped to mitochondrial genes and the fraction of reads mapped to ERCC spike-ins, all as a function of the total number of reads. Cells that passed quality control are marked by green circles, while black circles indicate cells that failed the quality control and were excluded from downstream analyses. d, The boxplots show the total log expression of normalized counts for XIST and Y-genes across all clusters. While XIST was mostly not detected, Y-chromosome genes had always non-zero counts; this suggests that there is no contamination from maternal tissues in any of the clusters. n = 1195 cells were examined from a single embryo. Horizontal black lines denote median values and boxes cover the 25^th and 75^th percentiles range; whiskers extend to 1.5 × IQR. e, The stacked barplots indicate the percentages of cells from each cluster in the phase G1, S or G2/M of the cell cycle, as predicted from their transcriptomic profiles. f, Insertion-deletion length and size distribution of gastrula and fetal liver data. Y axis represents total number of indels on merged cells, while x axis represents indel length in base pairs. Hemato-Endothelial Progenitors (HEP), Endoderm (End), Advanced Mesoderm (AM), Primitive Streak (PS), Extraembryonic Mesoderm (ExM), Axial Mesoderm (AxM), Erythroblasts (Ery), Emergent Mesoderm (EM), Epiblast (Epi), Nascent Mesoderm (NM), Ectoderm (Amniotic/Embryonic (EAE)).