Extended Data Fig. 8. The emergence of mesenchymal subtypes from the patterned mesoderm.
a, The predicted absolute number (log2 scale) of cells of each mesoderm cell type at each somite count. The predicted absolute number was calculated by the product of its sampling fraction in the overall embryo and the predicted total number of cells in the whole embryo at the corresponding timepoint. Because cell numbers were only predicted for the broader bins (Fig. 1b), rather than individual somite counts, these were used for roughly corresponding sets (0-12 somite stage: E8.5; 14-15 somite stage: E8.75; 16-18 somite stage: E9.0; 20-23 somite stage: E9.25; 24-26 somite stage: E9.5; 27-31 somite stage: E9.75; 32-34 somite stage: E10.0). For each row, the first somite count with at least 10 cells assigned that cell type annotation is labeled, and all observations prior to that somite count are discarded. b, Re-embedded 2D UMAP of 110,753 cells from the selected cell types of mesoderm (clusters 1-12 as listed in panel a) from 5-20 somite stage embryos. c, The same UMAP as in panel b, but with inferred progenitor cells colored by derivative cell type with the highest mutual nearest neighbors (MNN) pairing score. d, Normalized MNN pairing score between mesodermal territories (column) and their inferred derivative cell types (row) from 5-20 somite stage embryos. The selected cell populations are first embedded into 30 dimensional PCA space, and then for individual derivative cell types, MNN pairs (k = 10 used for k-NN) between their earliest 500 cells (in absolute time) and cells from mesodermal territories are identified. e, Re-embedded 2D UMAP of 275,000 cells from the selected cell types of mesoderm (clusters 1-18 as listed in panel a) from 26-34 somite stage embryos. f, The same UMAP as in panel e, but with inferred progenitor cells colored by derivative cell type with the highest MNN pairing score. g, Normalized MNN pairing score between mesodermal territories (column) and their inferred derivative cell types (row) from 26-34 somite stage embryos. The selected cell populations are first embedded into 30 dimensional PCA space, and then for individual derivative cell types, MNN pairs (k = 10 used for k-NN) between their earliest 500 cells (in absolute time) and cells from mesodermal territories are identified.