Fig. 8: Native BMEC identity is preserved in ex vivo culture.

a Scheme of experimental design for freshly isolated BM tdT⁺ and P0 WBM cultured cells. Parts of the figure (the femur) were drawn by using pictures from Servier Medical Art by Servier, licensed under a Creative Commons Attribution 3.0 Unported License. b, c UMAP plot of single-cell gene expression profile from fresh cells. Clusters ranging from 0 to 4 identified by PCA and nearest neighbors are displayed in b using different colors. c Level of expression, reported as z-scaled log2 counts per million (CPM), of Emcn, Tek, Lepr, and Ptprc are shown in blue for each cluster in the UMAP visualization. d Gene expression profile for the sinusoidal/arterial gene signature. The levels of expression are reported as z-scaled log2 counts per million (CPM). e Integrated UMAP plot of the single-cell gene expression profile of fresh sorted P0tdT⁺ (Emcn⁺ and Emcn⁻) (cyan) and cultured BMEC cells sorted at P0 (red). Numbers indicate clusters. f Level of Emcn expression, reported as z-scaled log2 counts per million (CPM), visualized in Integrated UMAP plot as in e. g, h Heatmaps of gene expression profiles in fresh and cultured BMECs using the arterial/sinusoidal signature (g) and the tip/stalk signature (h). Dendrograms above heatmaps show hierarchical clusters and the distance between the subpopulation’s transcriptomes. Results show differences between Emcn⁻ and Emcn⁺ and the linkage between freshly isolated and cultured cells of the respective groups. The levels of expression are reported as z-scaled log2 counts per million (CPM).