Extended Data Fig. 7: Spatial domains in limb mesenchymal cells.
From: A single-cell transcriptome atlas profiles early organogenesis in human embryos
a, UMAP and RNA velocity analysis of human forelimb at CS12 and CS15-16 (see Fig. 3 for conventions). b, Batch effect of embryo estimated by entropy of mixing at CS13-14 and CS15-16 (Methods, Mann-Whitney U test p < 2.2 × 10−16, n = 100 randomly sampled cells). The center line denotes the median, while the box contains the 25th to 75th percentiles. The whiskers mark 1.5x interquartile range. c, Normalized UMIs of top DEGs of domain m in domain m by embryo. d, UMAP of mouse forelimb at E10.5 and E12 by reclustering a published dataset27 (Supplementary Table 2). e, The expression of marker genes in each domain from human scRNA-seq (red), mouse scRNA-seq (blue), and mouse in situ data (black) at three stages. Mouse in situ data in each domain were manually classified to strong (large dot), weak (small dot) and no expression (no dot) based on in situ images. Domain m was not identified in E12 data of mouse. HOX genes (black boxes) show developmental stages are aligned between human and mouse datasets. f, The expression of specific markers of domain m on UMAP in human and mouse. Dashed circles, domain m. g, Left panel, UMAP co-embedding of CS15-16 of human and E12 of mouse colored by species and domains (see panel a for conventions). Right panel, the average percentage of mouse cells in k-nearest neighbors (KNN) of human cells in each domain in co-embedding space (Methods, mean +/− SEM, number of cells indicated above each bar). The first bar (background) denotes the percentage of mouse cells in total cells of human and mouse. Asterisks denote significant p values by Mann-Whitney U test (domain a, 3 × 10−7; domain b, 5 × 10−7; domain m, 9 × 10−9). In all panels, n = 1, 3, 3 embryos at CS12, CS13-14, and CS15-16, respectively.
