Fig. 8: Comparison of embryoids and of mouse embryos scRNA-seq transcriptomes.
From: Construction of a mammalian embryo model from stem cells organized by a morphogen signalling centre
a PCA of bulk RNA-seq generated from 5000 randomly selected cells from scRNA-seq of embryoids at D8 and mouse embryos at E7.5, E7.75, E8.0, E8.25, E8.5, E9.5 and E10.5. b Pearson correlation coefficient plot for D8 embryoids and mouse embryos in between E7.5 and E10.5 showed the highest correlation between the transcriptome of D8 embryoids (ebD8) and of E8.5 mouse embryos. c UMAP plots showing 6639 cells isolated from D8 embryoids and 8590 cells isolated from E8.5 mouse embryos. A unique colour was used to show cells of each cluster (prog.: progenitors, Inter.: intermediate). The surface ectoderm cluster was only present in mouse embryos. Clusters with a small number of cells were delineated by circles or by an oval line. d Dot plot graph showing both the percentage of cells (diameter of the dot) of a given cluster that expressed the marker gene of that cluster and its level of expression (gradient of colour, blue for embryoids, red for mouse embryos). Names of the 24 clusters are given at the left and name of the marker gene for each cluster are given at the bottom. For each cluster, mouse embryo data are given in red top and the embryoid data are given in blue. e Pseudotime differentiation trajectory analysis for neural and mesoderm trajectories in D8 embryoids.
