a Identification of four major clusters coloured by lineage via UMAP: epiblast (red, 108 cells at 9 d.p.f., 58 cells at 11 d.p.f., total=166), hypoblast (purple, 82 cells at 9 d.p.f., 54 cells at 11 d.p.f., total = 136), cytotrophoblast (green, 1956 cells at 9 d.p.f, 226 cells at 11 d.p.f, total=2182), syncytiotrophoblast (cyan, 1058 cells 9 d.p.f., 1278 cells at 11 d.p.f., total = 2336). Number of embryos: n = 8 at 9 d.p.f., n = 8 at 11 d.p.f. Only embryos with all three lineages were analysed, refer to Supplementary Data 1. b Heatmap displaying z-score values of the most differentially expressed genes between different lineages, alongside known lineage markers. In bold red the top most enriched genes expressed in a particular lineage as shown in Supplementary Data 2. c Comparisons between pre-implantation single-cell sequenced epiblast and ICM cells previously published33,34,35,36 (cyan inner cell mass (ICM) at 5 d.p.f., green epiblast at 6–7 d.p.f.) versus our post-implantation datasets (purple epiblast at 9 d.p.f, red epiblast at 11 d.p.f.). Comparison of the expression levels of key markers of naïve pluripotency (d), primed pluripotency (e) and core pluripotency (f). Bars represent median. g Logistic regression analysis showing quantitative cell matching scores between human embryo datasets ICM at 5 d.p.f. (blue), pre-Epi at 6–7 d.p.f. (green) and post-Epi at 9 d.p.f. (purple) and at 11 d.p.f. (red) (y-axis) and human embryonic stem cells H9 and H9-Reset43 (x-axis). Comparison H9 vs H9-Reset by Sidak’s multiple comparisons ad-hoc test for 2 way ANOVA, H9 cells differ from the H9-Reset throughout stages: 5 d.p.f. (p = 0.0015**), 6–7 d.p.f. (p < 0.0001****), 9 d.p.f. (p = 0.0101*) and 11 d.p.f. (p < 0.0001****). This difference is highly significant at 6-7 d.p.f., with H9-Reset cells sharing similarities to 6–7 d.p.f. pre-implantion epiblast, and at 11 d.p.f. with H9 cells sharing similarities with 11 d.p.f. post-implantion epiblast.