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. Author manuscript; available in PMC: 2023 Aug 26.
Published in final edited form as: Science. 2023 Aug 18;381(6659):eadd7564. doi: 10.1126/science.add7564

Fig. 5. Accelerated macrophage production in YS and iPSC culture.

Fig. 5

(A) Left: Line graph of monocyte and macrophage proportions in YS scRNA-seq across time. Dashed line indicates pre- and post-AGM stages. Middle: Milo beeswarm plot showing differential abundance of YS scRNA-seq myeloid neighbourhoods across time. Color shows degree of enrichment (blue: early, red: later) (data S4 and S24). Right: Bar chart of YS scRNA-seq myeloid cell state proportions across time. Mono–mac int. monocyte macrophage intermediate. (B) Dot plot showing the mean expression (color) and proportion of cells expressing monocyte marker genes (dot size) in EL monocytes and YS myeloid cell states. Genes include YS vs EL monocyte DEGs and established monocyte markers (data S17). (C) Left: FDG of macrophage trajectory in YS scRNA-seq, colored by cell state, overlaid with PAGA showing monocyte-independent <CS14 (pre-AGM; n=2; k=3,561; top) and monocyte-dependent trajectories >CS14 (post-AGM; n=6; k=35,962; bottom) (data S5). Right: FDG overlaid with scVelocity directionality, colored by cell cycle gene enrichment (GO:000704 module). (D) Heatmap of regulons associated with trajectories in C. TFs discussed in text highlighted (turquoise: pre-macrophage; purple: monocyte-dependent). (E) Dot plot showing the mean expression (color) and proportion of cells expressing macrophage and microglia marker genes (dot size) in myeloid cell states in YS, AGM (12), skin (49), gonad (50), and brain (56) fetal scRNA-seq datasets (data S13 and S31). (F) Heatmap of significant (P<0.05) CellphoneDB-predicted interactions between YS scRNA-seq TREM2+ macrophages and ECs (data S28). Color represents z-scored expression of gene pairs, brackets indicate top curated interactions for cell-state pairs. (G) FDG of macrophage trajectory in iPSC scRNA-seq (20), colored by cell state, overlaid with PAGA showing monocyte-independent <D21 (n=5; k=779; left) and monocyte-dependent >D21 (n=7; k=8,553; right) transitions (data S7 and S5). (H) Heatmap of regulons associated with iPSC macrophage trajectories shown in G. TFs discussed in text are highlighted as in D.