Extended Data Fig. 5: Merged clustering of RNA-seq Day 0 – Day 5 of the embryoids.
From: Modelling post-implantation human development to yolk sac blood emergence
(a) UMAP showing the merged clusters annotated by day. (b) UMAP showing the merged clusters with unsupervised clustering applied. (repeated figures: The WT clusters are shown in Fig. 2a Cluster 14 is the amnion-like cluster shown in Fig. 2b; Cluster 6 is the D2 anterior-like cluster shown in Fig. 3a; Cluster 2 is the D3-5 anterior-like cluster shown in Fig. 3a; and Cluster 15 is the posterior-like cluster shown in Fig. 3b.). (c) Heatmap showing the top 20 genes corresponding to each cluster of the merged day 0 through day 5 dataset. (d) Gene set enrichment analysis on the genes with greater than 2-fold upregulation in the D2 anterior-like cluster (5) as compared to the day 3–5 anterior-like cluster (2) using the indicated pathway reference datasets. All top pathways identified correspond to cell cycle, suggesting the separation observed in the UMAP is mainly attributable to differences in proliferative state. Combined score was obtained via Enrichr and was computed by taking the log of the p-value from the Fisher exact text (one-sided) and multiplying it by the z-score of the deviation from the expected rank.
