Figure 2. Characterization of BM resident cell types.
a, Gene expression levels of Sca1, Endomucin (Emcn), Nestin, and Ng2, with relevant populations colour-coded. MAGIC47 was used for imputation of drop-out values. b, Deep imaging of a BM section immunostained with antibodies against Sca-1 and Emcn. Scale bar = 20 μm. c, Enrichment of gene expression signatures of Ng2+ MSCs, Adipo-CAR and Osteo-CAR cells in previously published transcriptomes of relevant genetically labelled populations5,7–9. See Figure S4b for further populations, and the supplementary note for a detailed evaluation of the algorithm used (CIBERSORT). Error bars indicate the standard error of the mean across n=3 bulk transcriptome samples per class. d, Boxplots of the scaled expression level of selected genes in single cells from the Adipo-CAR, Osteo-CAR and Osteoblast populations. For the right panel, the mean expression of all genes annotated with the gene ontology term ‘ossification’ was computed for each cell. e, Projection of all mesenchymal cell types using PHATE48 with time derivatives of gene expression state, as determined by RNA velocity22, highlighted as arrows. f, Comparison of cell type frequencies between distinct cell isolation methods used for scRNAseq.