Fig. 3: The transcriptomes of IVC day 9 embryos closely resemble those of E8.5 embryos.

A Uniform manifold approximation and projection (UMAP) analysis of scRNA-seq data at the indicated timepoints for E6.5 and E8.5 embryos and IVC day 9 (D9) embryos. B UMAP plot showing the cell atlas. Cells are colored according to their cell-type (see legend below). E6.5 (14,315 cells), E8.5 (14,761 cells), D9 (10,756 cells). A comparison of cell-type proportions between E8.5 embryos and IVC day 9 embryos. D9: IVC day 9. C Heatmap showing the global level of similarity across all identified tissues between D9 and E8.5 embryos. D Cell type proportions for E6.5 and E8.5 embryos and IVC day 9 embryos. E Violin plots depicting genes that were upregulated and downregulated across 19 fractions in D9 embryos relative to E8.5 embryos. F UMAP analysis of scRNA-seq data for the heart regions of E8.5 and D9 embryos. G Localization of first heart field (FHF) and second heart field (SHF) on the UMAP in (A) based on expression of TBX5, HCN4, NKX2.5, HAND1 for FHF and TBX1, SIX1, SIX2 for SHF. H Bubble plot showing a curated list of marker genes that were used to identify the first heart field and second heart field. I UMAP plot of reclustered multipotent progenitor populations, colored by cluster. AHF, anterior heart field; pSHF, posterior second heart field; BMP, branchiomeric muscle progenitors. J Bubble plot showing a curated list of marker genes that were used to identify the posterior second heart field, anterior heart field, and branchiomeric muscle progenitors.