Schematic of the single-copy assay workflow. A monomer in each HOR (red box) or single-copy reference gene on the same chromosome (dark blue box) in a subclone is isolated by restriction enzyme digestion, partitioned into more than 18,000 droplets, and simultaneously amplified using HOR-specific or single-gene primers (black arrows) in separate reactions (TableS1). The droplets that contain targets (green peaks) are counted by signal amplitude, and the CN is calculated. The HOR CN per array is determined by normalization with single-gene copies (e.g., HOR copies/single-gene copies).
