Single-cell multiomics profiling of pediatric KMT2A-r leukemia. (A) Experimental design of multiomics profiling of KMT2A-r leukemia and healthy donor samples. (B) Sorting strategy for capturing blasts and nonmalignant cells from B-ALL patients. (C) Number of assays/samples performed for each single-cell omics protocol. (D) Overall UMAP of all scRNA-Seq cells (left panel) and all scATAC-Seq cells (right panel) of 18 infant ALL samples, colored by assigned cell populations. Total numbers of sequenced cells are indicated. (E) Cell type compositions based on the scRNA-Seq and scATAC-Seq data in panel D. (F) Heatmap of differentially expressed genes for each cell population compared with the rest of populations [abs(Log2[FC]) >0.5 and FDR <0.05]. Values in the heatmap are row-wise Z-scores. Color code for each cell population is the same as in panel D. (G) Heatmap of enriched TFs at ATAC-Seq peaks. Enrichment is represented by the normalized deviation scores (z-score) calculated by chromVAR. (H) Genome browser tracks and gene expression violin plots for representative cell-type-specific marker genes. Left panels, aggregated scATAC-Seq signals for each assigned cell type. Right panels, normalized scRNA-Seq expression values for the corresponding cell type. (I) Schematic of scTLR-Seq for detecting fusion transcripts in single cells. (J) Fraction of cells with KMT2A fusion and wild-type reads for each cell population, including blasts, mature B cells, monocytes, NK/T cells from patients, and hematopoietic cells from healthy donors, defined as the ratio of the number of cells with KMT2A reads vs the total number of sequenced cells of a given population.