Fig. 1: scRNA-seq profiling of the in vitro PGCLC differentiation system.
From: Enhancer-associated H3K4 methylation safeguards in vitro germline competence
a Schematic representation of the in vitro PGCLC differentiation system. Embryonic stem cells (ESC) are differentiated into epiblast-like cells (EpiLC). Day 2 (d2) EpiLC are germline competent and can be differentiated into embryoid bodies (EB) containing primordial germ cell-like cells (PGCLC). In contrast, the progress of EpiLC into epiblast stem cells (EpiSC) restricts germline competence. The diagram to the far right illustrates the in vivo location of PGCs at the proximal-posterior end of a mouse embryo (ExE: Extraembryonic Ectoderm; ExM: Extraembryonic Mesoderm, PGC: Primordial germ cells). b t-SNE plot of the scRNA-seq data (n = 2782 cells) generated across the main stages of the in vitro PGCLC differentiation protocol. c t-SNE plot based on the scRNA-seq data generated in d4 EB (n = 368 cells). K-means clustering of d4 EB identified four clusters resembling the transcriptomes of PGCs and their main surrounding tissues in vivo: ExE, ExM, and Endothelial cells. d Gene expression summary for the different gene sets defined using the scRNA-seq data (see Methods). The number of genes in each set is indicated below and the size of a dot represents the average expression of all genes within a gene set for the indicated cellular stages (UMI: unique molecular identifier). e Heatmap showing the expression of selected genes from the gene sets shown to the left (i.e. ESC, EpiLC, EpiSC, and PGCLC gene sets) within individual cells belonging to the indicated cellular stages. The expression values are displayed as UMI counts. f t-SNE plot for the d2 EpiLC scRNA-seq data alone (n = 289 cells). g Violin plots showing transcriptional noise (defined as cell-to-cell transcript variation for the 500 most variable genes) for ESC, EpiLC, and EpiSC. Lower transcriptional noise indicates higher transcriptional similarity between the cells belonging to a particular stage. All cellular stages shown were compared to d2 EpiLC using two-sided Wilcoxon tests (*p-value < 2.2 × 10−16). The horizontal line in the boxplots indicates the median, the box indicates the first and third quartiles and the whiskers indicate ± 1.5 × interquartile range.
