Fig. 2

Single-cell transcriptomics from forelimb autopod and zeugopod. a Schematics of forelimb territories harboring different combinations of Hoxd gene activity. Single-cell RNA-seq was performed on micro-dissected 12.5 forelimb autopod (AP, blue) and zeugopod (ZP, yellow) tissues derived from Hoxd11::GFP limbs and positive for GFP. b T-distributed stochastic neighbor embedding (tSNE) plot of gene expression relationships amongst the 199 single cells from AP (blue) and ZP (yellow) shows a segregation along the tSNE2 axis. c MA plot produced from cross-analysis between AP and ZP cells. Known genes with differential expression between tissues are indicated on the graph. d Gene nodes from the differentially expressed genes (DEG) upregulated in autopod tissue, as computed using co-expression and interaction meta-analysis. e Cumulative combinatorial expression of Hoxd genes in the autopod cells indicating variability of gene expression across Hoxd genes from cell to cell. f Spearman’s rank correlation heatmap and hierarchical clustering of genes that covaried with at least one posterior Hoxd gene in the autopod cells. Below are shown the names of Hoxd genes (bold) and their known target genes