Extended Data Fig. 9: Epiblast development during embryo culture in the 3D condition.
From: A developmental landscape of 3D-cultured human pre-gastrulation embryos
This figure relates to Fig. 4. a–d, Dynamic expressions of pluripotent genes over human embryo development in the 3D condition. a, The dynamic expressions of OCT4, TFCP2L1 and KLF4 during human embryo development (3 out of 3 embryos). b, The dynamic expressions of OCT4, SOX17 and KLF17 during human embryo development (3 out of 3 embryos). Loss of TFCP2L1, KLF4 and KLF17 at 10 d.p.f. (implantation stage) indicate the pluripotent state transition of epiblasts. c, Expression of NANOG and PRDM14 at 10-d.p.f. human embryos (2 out of 2 embryos). d, Dynamic expressions of OCT4, CD24 (a primed pluripotency gene) and KLF17 during human embryo development (2 out of 2 embryos). e, t-SNE of pluripotent stem cells. To exclude cells from the AME and intermediate state in the epiblast cluster, we excluded the NANOG-negative cells and maintained 136 cells with high expression of NANOG. f, The violin plots show the dynamics of naive, primed and common pluripotency genes in pre-gastrulation embryos. All violins have the same maximum width, black dot denotes the mean. AME and intermediate state cells were excluded in the synthesis. *P < 0.05, **P < 0.01, ***P < 0.001, two-sided Wilcoxon rank-sum test. g–j, PluriNetWork analysis of EPIs from ICM (g), pre-EPI (h), post-EPI (i) and PSA-EPI (j) stages revealed that key pluripotency regulators dominated the networks. k, DEGs during EPI development. GO terms and representative genes in DEGs in the pairwise comparisons are indicated. l–n, Scatter-plot comparison of the gene-expression levels between ICM and pre-EPI (l), pre-EPI and post-EPI (m), and post-EPI and PSA-EPI (n). Key genes are annotated (Supplementary Table 6). Red denotes upregulated; green denotes downregulated; >twofold difference, uncorrected P < 0.01 (likelihood ratio test) and median FPKM > 1 in one group. Scale bars, 50 μm (a, b), 100 μm (c) or 25 μm (d).
