Fig. 2: Single-cell characterization of Cxcl12-creER⁺ BMSCs.

a Single-cell RNA-seq analysis, UMAP-based visualization of major classes of Cxcl12-GFP⁺ cells (Clusters 0–8). Red dotted contour: reticular cells (Cluster 0). Center panels: tdTomato expression, feature plot (top), violin plot (Clusters 0–2) (bottom). Right panels: feature plots. Blue: high expression. n = 5858 cells merged from two biological replicates (Mouse #1: 2028 cells, Mouse #2: 3830 cells). b Split-dot-based visualization of representative gene expression in Cluster 0 (C-0, reticular cells) and Cluster-1 (C-1, pre-osteoblasts). Upper: Mouse #1, Lower: Mouse #2. Circle size: percentage of cells expressing a given gene in a given cluster (0–100%), color density: expression level of a given gene. c–f CFU-F assay. c Cxcl12^CE-tdTomato⁺ (left) and Ubc^CE-tdTomato⁺ (right) bone marrow cells at P28 (pulsed at P21). Scale bar: 5 mm. d percentage of tdTomato⁺ colonies among total CFU-Fs. n = 4 (Cxcl12^CE), n = 7 (Ubc^CE) mice. **p < 0.01, two-tailed, Mann–Whitney’s U test. Data are presented as mean ± s.d. e Survival curve of individual tdTomato⁺ clones over serial passages. n = 26 (Cxcl12^CE), n = 48 (Ubc^CE) clones. Gehan–Breslow–Wilcoxon test. f In vitro trilineage differentiation assay of Cxcl12^CE-tdTomato⁺ clones (Passage 2–7). Upper panels: Adipogenic conditions. LipidTOX staining (left). Green: LipidTOX-Alexa488, red: tdTomato. Oil red O staining (Right). Center panels: Osteogenic conditions. Green: Col1(2.3 kb)-GFP, red: tdTomato. Alizarin Red staining (right). Lower panel: Chondrogenic conditions, Alcian Blue staining. Insets: differentiation medium negative controls. Scale bar: 200 µm. n = 12 clones. Source data are provided as a Source Data file.