Figure 7. Validation of the presence of a “stem-like” cell cluster from an independent study of atherosclerotic mice.
A recently published single-cell data set from Kim et al. (ref. 40; “Kim”) from sorted CD45+ cells isolated from whole aortas of Ldlr–/– mice fed WD for 12 weeks was combined with our progression and regression data sets (Lin Progression, Lin Regression) with Seurat merging and aligned with canonical correlation analysis (CCA). (A) t-SNE visualization of the 8906 single cells from both data sets after Louvain clustering and colored by sub-cluster.(B) SingleR method was used for unbiased cell classifications of each sub-cluster against the ImmGen database and colored and labeled accordingly on the t-SNE plot. (C) t-SNE plot colored based on experimental group and data sets, showing that cluster 6 includes cells from all 3 experiments. (D) Cluster composition by cell numbers of experimental groups and data sets (red, Kim Ldlr–/–; green, Lin Progression; blue, Lin Regression) in total single cells. (E) Violin plot and heatmap showing the highest expression of cell cycle (“Stemness”) genes in cluster 6. (F) Violin plot and heatmap showing the expression of CX3CR1 in cluster 6.