Extended Data Fig. 1: Construction of the MCDA.

a, Hierarchical trees showing the relationship between 95 cell types in MCDA, colored by lineage. b, t-SNE visualization of 520,801 single cells from seven developmental stages of mice, colored by lineage. They share the same color legend of lineages. c, t-SNE visualization of 520,801 single cells from different developmental stages of mice, colored by tissue. d, Heatmaps showing the number of differentially expressed genes (DEGs) in each developmental stage across the ten tissues of mice. DEGs between two stages of cells were identified using a Wilcoxon rank sum test. e, Summary of the GO enrichment analysis performed on the DEGs in each developmental stage. f, Visualization of the top 10 principal components of PCA in MCDA. Colors represent tissues, which is the same in Extended Data Fig. 1c. g, Lollipop chart displaying the gene expression variance explained by residuals (that is, biological and technical noise) or experimental factors such as tissue, stage, gender, and their respective combinations. Items like “tissue and gender” are variances explained by interactions of two factors instead of the union of two factors. h, UMAP visualization of 57,118 single cells in the kidneys at 7 different time points, colored by stage. i, Summary of the GO enrichment analysis performed on the DEGs in the kidneys across different stages. The red marks the go terms related to physiological functions of renal functions.