Fig. 2: Identification of BM cell subsets in Control, CHIP, and MDS by scRNA-seq. | Nature Communications

Fig. 2: Identification of BM cell subsets in Control, CHIP, and MDS by scRNA-seq.

From: Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia

Fig. 2

A Schematic of the experimental design using donor-derived BM aspirates and FFPE trephine bone biopsies. Created in BioRender. Prummel, K. (https://BioRender.com/kdi1w0u). B Uniform manifold approximation and projection (UMAP) of 24,639 cells across the major cell populations of scRNA-seq from donors highlighted in Fig. 1A and Fig. 2A, colored by Donor ID and split by condition. C UMAP of 12,557 HSPCs, with clusters annotated by cell type. D Dot plot of marker gene expression in HSPCs. Circle size corresponds to percent of cells expressing the given gene and color the expression level. The heatmap shows average AUCell scores of marker transcription factors based on regulons inferred in this study. E UMAP of 9,962 T cells, with clusters annotated and colored by cell type. F Dot plot of T cell marker expression and heatmap of average AUCell scores65. G UMAP of 1,396 stromal cells integrated between 10x and CEL-Seq2 data, colored by cell type annotation. H Dot plot of stromal cell markers. I Average expression of genes upregulated in MDS vs. Control in the NanoString data, shown across our scRNA-seq cell type clusters. Source data are provided in the Source Data file and Supplementary Data 7.

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