Table 1. QC metrics summary for experiments displayed in Figure 1.

Source type	FACS depletion	N pass QC	Median N fragments	Median mitochondrial reads	Median unique	Median in TSS	Median in peaks
Nuclei	Unsorted	4719	7344	43 | 0.6%	5247 | 71.6%	1332 | 24.9%	2306 | 43.9%
Nuclei	Dead/debris	5526	10,526	59 | 0.6%	7284 | 69.4%	2186.5 | 30.1%	3647 | 50.5%
Nuclei	Dead/debris/neutrophils	7769	19,972	136 | 0.9%	11,528 | 59.1%	4846 | 41.5%	7503 | 64.8%
Permeabilized cells	Unsorted	6329	5541	100 | 1.9%	3308 | 59.8%	871 | 26.4%	1390 | 42.2%
	Dead/debris	6956	6733.5	120 | 2.0%	3795.5 | 56.8%	1219.5 | 32.6%	1874 | 50.2%
	Dead/debris/neutrophils	9849	14,069	514 | 4.0%	4756 | 34.3%	2536 | 54.4%	3650 | 76.8%
For all metrics to the right of median N fragments, both the absolute number and a percentage are provided. Median % mitochondrial and median % unique were calculated as a fraction of total fragments; % in TSS and % in peaks were calculated as a fraction of unique fragments. TSS: transcription start sites; FACS: fluorescence-activated cell sorting.