For the bulk data analysis, we obtained DNase hypersensitivity peaks from the Roadmap Epigenomics Project. MACS222 peaks for blood cells (Primary monocytes from peripheral blood, Primary B cells from peripheral blood, Primary T cells from peripheral blood, Primary Natural Killer cells from peripheral blood, Primary hematopoietic stem cells G-CSF-mobilized Female, Primary hematopoietic stem cells G-CSF-mobilized Male, and Monocytes-CD14+ RO01746 Cell line) were downloaded from the Epigenomics Roadmap Portal18. For the single cell ATAC-seq data, peaks were called for each cell line or type using MACS2 applied to the merged single cell ATAC-seq data. All peaks were re-sized to a uniform width of 500 bp, centered at the summit. For both the set of peak calls from the blood cells in Roadmap and the set of peak calls from the scATAC-seq data, peaks were combined by removing any peaks overlapping with a peak with greater signal. Peak width was chosen based on typical sizes of ATAC-seq peaks across a wide collection of experiments, although chromVAR is fairly robust to the exact size of the peaks used (Figure S5, Supplementary Note 2).
