scRNA-seq analysis of LSK cells from sham and CL&P mice. Related to Fig. 2. (A) Experimental procedure for scRNA-seq analysis. B6 mice were operated by sham or CL&P surgery. 12 wk later, BM cells were harvested from three sham and three CL&P mice, respectively, and LSK cells were sorted for scRNA-seq. (B) Gating strategy for FACS sorting LSK cells. (C) Unsupervised clustering of LSK cells visualized by a UMAP plot of merged sham and CL&P datasets. (D) Heatmap of expression of the top DEGs per cell state (row) in each cell (column). Expression of each gene was Z score transformed across the cells displayed in the heatmap. Dendrogram indicates the result of hierarchical clustering on genes expressed in the heatmap. (E) UMAP projection of scaled expression of gene signatures distinguishing HSCs, MPP2, MPP3, MPP4, and cycling cells. At right, a UMAP plot of merged sham and CL&P datasets shows cell-state clustering of LSK cells based on the expression of HSC and MPP signature genes. (F) UMAP projection of scaled expression of published gene signatures of HSCs, MPP2, MPP3, and MPP4 cells (Klein et al., 2022).