Extended Data Figure 8. Stromal cell heterogeneity in FBM.

8a) UMAP of FBM scRNA-seq stromal cells (k=6,287). Dotted lines indicate broad lineages. Abbreviations: mac = macrophage; Fb = fibroblast; pre. = precursor.

8b) Dotplot showing cell state-defining genes for osteoclasts and macrophages in the FBM scRNA-seq dataset. Methods/interpretation as in Fig. 1b.

8c) Dotplot showing cell state-defining genes for osteochondral-lineage cells in the FBM scRNA-seq dataset. Methods/interpretation as in Fig. 1b.

8d) Barplot showing frequency of stromal cell states in FBM scRNA-seq samples. Samples are grouped into 4 developmental stages to facilitate statistical comparison over gestational stage. P-values resulting from quasibinomial regression model (subject to one-sided ANOVA; with correction for sort gates; computed at 95% CI and adjusted for multiple testing using Bonferroni correction) are shown in parentheses; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001; Supplementary Table 19, 45).

8e) Heatmap showing gene enrichment (see Methods) of postnatal mouse BM stromal cell¹⁹ signatures in human FBM scRNA-seq stromal cells (coloured as in panel a).

8f) Dotplot showing cell state-defining genes for EC in the FBM scRNA-seq dataset. Methods/interpretation as in Fig. 1b.

8g) Left panel: Violin-plot showing expression of genes with documented role in sinusoidal EC function⁴in sinusoidal ECs from FBM and FL scRNA-seq datasets. Right panel: Equivalent protein dotplot where marker was present in CD34⁺ CITE-seq ADT panel. Asterisks indicate DEGs (two-sided Wilcoxon rank-sum statistical test with Benjamini-Hochberg procedure for multiple testing correction; *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001; Supplementary Table 46-47). Methods/interpretation as in Fig. 3a, c (upper limit of 5.5 for protein dotplot).

8h) Heatmap showing expression of mouse BM EC DEGs from Baryawno et al (see Supplementary Methods) in FBM scRNA-seq ECs. GEX values are log-transformed, normalised and scaled (upper limit of 3). Hierarchical clustering for each cell type is shown (see Methods).

8i) Heatmap of differentially enriched inflammatory and cytokine production pathways in DS vs. non-DS FBM scRNA-seq stroma defined by a two-sided Wilcoxon rank-sum test with Benjamini-Hochberg procedure for multiple testing correction; Supplementary Tables 20, 43).