Fig. 2: Characterization of human limb bud mesenchyme and epithelium.

a UAMP visualization of the ten subsets in 5 WPC limb buds. b Hierarchical clustering of the mesenchymal and epithelial subsets using top 50 principal components (PCs). c The inferred relationships among the mesenchymal and epithelial subsets in PAGA layout. d Stacked bar charts showing the cell cycle distributions in the mesenchymal subsets. e Enriched GO terms of differentially expressed genes (DEGs) in the mesenchymal subsets. f Heatmap showing expression of curated HOX genes scaled across the mesenchymal subsets. Hox genes were clustered into two branches based on hierarchical clustering of the rows, as indicated in green and purple. g Visualization of the mesenchymal subsets (left) with UMAP plots showing the expression of curated PD and AP marker genes (right; Proximal, MEIS2; Distal, HOXD13; Anterior, IRX3; Posterior, SHH). h GSVA analysis of pathway enrichment in the proximal and core mesenchyme (LBM3/OCP) and distal mesenchyme (LBM1/2). T values for each pathway were shown (two-sided unpaired limma-moderated t-test). i Heatmap showing the area under the curve (AUC) score of regulons enriched in the mesenchymal subsets (left). Z-score (row scaling) was computed. Representative regulons were shown on the right. The number of predicted target genes for each regulon was shown in the parenthesis. Hierarchical clustering on columns indicated correlation between cell subsets. Binary activities of representative regulons were shown by UMAP plots (right).