Varieties of cellular hierarchies in NUP98r leukemia. (A) Strategies for scRNAseq and deconvolution of bulk RNAseq data. (B) UMAP plots of patient samples colored by sample source (left) and transcriptional clusters (right). (C) Enrichment of cells in each cluster indicated by colors and sizes (left), and marker gene expression indicated by colors (averaged expression) and size (ratio of expressing cells: count >0 (right). (D) UMAP plot of reference bone marrow and thymocyte scRNAseq data, colored according to cell labels from the original reference data.⁴³ (E) Distribution of patient sample scRNAseq on the reference data inferred by the MapQuery function in the Seurat package. Cells in normal hematopoietic cell clusters were excluded. Cells are colored according to the cell density on the UMAP plot. Cooperating mutations found in bulk samples are also shown. (F) Enrichment of cells with each cell label inferred by Seurat, indicated by colors and sizes. (G) Cellular component of bulk RNA samples (n = 185) inferred by CIBERSORT using a signature matrix derived from reference scRNAseq data. Bars are colored by cell populations in each sample. cDC, classic dendritic cell; CLP, common lymphoid progenitor; DP, CD4-CD8 double-positive T cell; GMP, granulocyte-monocyte progenitor; HSPC, hematopoietic stem and progenitor cell; NK, natural killer T cell; pDC, plasmacytoid dendritic cell; UMAP, uniform manifold approximation and projection.