Fig. 4: Niche cell transcriptional heterogeneity in mice with CXCR4-deficient MPPs.
a UMAP visualization of bone marrow non-hematopoietic cells. b Expression levels of genes associated with endothelial cells (Cdh5), MSPCs (Lepr), and osteolineage cells (Col1a1) overlaid on UMAP. c Overlay of UMAP visualization of bone marrow non-hematopoietic cells from Flk2-cre.Cxcr4fl/+ (CTR, red) and Flk2-cre.Cxcr4fl/fl (KO, blue) mice. d Cluster proportion. e Differential abundance test with Milo. UMAP cluster representation (left); graph representation of Milo differential abundance testing (middle); Beeswarm plot showing the distribution of logFC in neighborhoods containing cells from different Seurat clusters (right). Nodes are neighborhoods colored by logFC between CTR and KO. Non-differential abundance neighborhoods (FDR 5%) are colored white; neighborhood sizes correspond to number of cells in each neighborhood. Graph edges represent the number of cells shared between adjacent neighborhoods. Cell cluster frequencies in each sample (horizontal-colored bars). f Violin plots representing expression levels of essential HSC regulators (Kitl, Cxcl12, Ptn, Vcam1, Icam1) in CTR (red) and KO (blue) cell clusters.
