Fig. 3

scRNA-seq analyses reveals that the pro-inflammatory macrophages are enriched in the BALB/c limb following HLI surgery. A UMAP plots illustrating the distribution of macrophages (depicted in blue) and other cells (depicted in grey) from C57BL/6 and BALB/c mice at specified time intervals. The left UMAP plot aggregates all cells from the two strains across all time points. In the right-hand UMAP plots, macrophages for the distinct time points and individual strains are highlighted in blue, while all remaining cells are represented in grey. B The inflammatory gene module score is high in cluster 5 cells, which are specific to BALB/c mice. Red color indicates high gene module score. C GSEA enrichment analysis reveals that M1 macrophage markers are highly expressed in BALB/c macrophages, while M2 macrophage markers are highly expressed in C57BL/6 macrophages. Macrophage gene expression patterns are assessed using scRNA-seq data. D Dot plot showing differentially expressed genes in macrophages between C57BL/6 and BALB/c mice on day 3 post-ischemia. Dot size represents -log10 FDR; color scale indicates log2-fold change in gene expression. Pink and blue colors indicate genes upregulated in C57BL/6 and BALB/c, respectively. E Volcano plot displaying differentially expressed genes from bulk RNA-seq analysis of macrophages purified from BALB/c and C57BL/6 mice at 3 days post-HLI. Red and blue dots represent upregulated genes in C57BL/6 and BALB/c mice, respectively. F: Genome browser snapshots showcasing bulk RNA-seq data at specified gene loci in macrophages derived from both strains on day 3 post-injury. Two biological replicates (rep1, rep2) are included for each condition. G Top five GO terms enriched by differentially expressed genes (FDR < 0.05, log2FoldChange>1) from panel E. Red and blue bars correspond to GO terms enriched in C57BL/6 and BALB/c mice, respectively