Supplementary Figure 12: Validation of enhancer cytometry in AML cell lines and primary cells by single-cell ATAC-seq.

(a) Enhancer cytometry of ATAC-seq data as shown in Figure 6a but ordered by patient instead of by AML cell type. (b) Projection of downsampled bulk hematopoiesis data onto a 2D PCA. Bulk ATAC-seq data were downsampled to give 1,000 fragments, approximately the lower bound of fragments obtained by scATAC-seq. Each dot represents an individual permutation of downsampled bulk ATAC-seq data from HSCs (green), GMPs (yellow), and monocytes (orange). Principal components were derived from bulk ATAC-seq data for normal hematopoietic cells. (c) Projection of downsampled bulk hematopoiesis data onto a one-dimensional myelopoietic differentiation trajectory. (d,e) scATAC-seq data derived from FACS-purified LMPPs (n = 94) (d) and monocytes (n = 88) (e) projected onto a 2D PCA plot. Principal components were derived from bulk ATAC-seq data for normal hematopoietic cells. (f) Enhancer cytometry of bulk ATAC-seq data derived from various blood cell lines demonstrates mixed regulatory contribution from various normal hematopoietic cell types. (g) Projection of scATAC-seq data derived from healthy monocytes, LMPPs, and leukemic cell types from patients SU070 and SU353 onto a one-dimensional myeloid differentiation trajectory. (h) Projection of scATAC-seq data derived from HL60 cells (n = 90) onto a one-dimensional myeloid differentiation trajectory. (i,j) Projection of scATAC-seq data derived from single cells of the common cell lines K562 (n = 227 total) and TF1 (n = 56) (i) and GM12878 (n = 75) (j) onto a one-dimensional erythroid (i) and lymphoid (k) differentiation trajectory. AU, arbitrary units.