Extended Data Fig. 7: Gene expression profiles of inflammasome components in the bone marrow stroma.
From: A stromal inflammasome Ras safeguard against Myc-driven lymphomagenesis
a. UMAP visualizations of CD45- (Ptprc-) osteoblast, perivascular, and vascular bone marrow niche cells (n = 19,418) taken from Tikhonova A.N. et al.38. Top: Labeled and color-coded according to algorithmically determined clusters (Seurat clusters). Bottom: Labeled and color-coded according to bone marrow niche (VECAD = vascular, LERP = perivascular, COL1A1 = osteoblast), as determined by the expression of niche marker genes Cdh5 (VECAD), Lepr, and Col1a1. b. UMAP visualization of bone marrow niche cells colored according to the normalized expression of niche marker genes (Cdh5 = vascular, Lepr = perivascular, Col1a1 = osteoblast). c. Violin plots of normalized expression of niche marker genes across all clusters of CD45- (Ptprc-) bone marrow niche cells. d. Table shows our manual cluster annotations of the original Seurat clusters generated from the scRNA-sequencing dataset by Tikhonova A.N. et al.38. Bone marrow endothelial cells (BMEC), mesenchymal stromal cell (MSC), leptin-receptor (LEPR), and osteoblasts. Sub-markers used were based on Tikhonova A.N. et al.1: BMEC: V1 Ly6ahigh and V2 Stab2high and indicated as LEPR+ when applicable for Seurat clusters 6 and 15. LepR MSC: sub-marked as O1, O2, O3 based on low co-expression of Col1a1 or V1, V2 based on low co-expression of VEcad. Osteoblasts: O1 Col16a1highTnnhigh, O2 Fbn1highIgf1high, O3 BglaphighCar3high, low for osteoblast maturation marker (Bglaplo) or when co-expressing Lepr (Seurat clusters 11 and 14). e. Dot plot of the expression of genes of interest (columns) in annotated CD45– (Ptprc–) bone marrow niche cell clusters (rows). Dot size indicates the percent of cells within a cluster that have non-zero expression of the corresponding gene. Dot color corresponds to scaled average normalized expression of a gene within a cluster.
