Figure 4.

Transcriptional landscape and heterogeneity of BMSCs at single-cell resolution

(A) Schematic overview of bone sample preparation for scRNA-seq.

(B–D) t-SNE plot with color-coded subclusters. Cell numbers are indicated for each cluster (B). Heatmap of the top-six most-significantly expressed genes in all clusters (C) and violin plots of individual cluster markers (D).

(E) Tile-scan confocal image of 3-week-old femur stained for EMCN (blue) PDGFRβ⁺ (red) mark and ACAN (green, chondrocytes). Arrowheads indicate PDGFRβ⁺ smooth muscle cells covering arteries.

(F and G) t-SNE plot with color-coded BMSC subclusters (F). Expression of mesenchymal (Pdgfrb, Pdgfra, Lepr, and Esm1), osteogenic (Hey1, Sp7, Postn, Runx2, and Bglap3), and proliferative (Mki67) marker genes in BMSC subclusters (G).

(H and I) Monocle trajectory analysis of BMSC lineage differentiation. Clusters are colored according to their identity (H) and relative expression of key genes is displayed in pseudo-time (I).

See also Figure S5