Table 1.

Quality control metrics to assess the impact of pre-encapsulation protocols

	MACS Enzyme on Minced Tissue	Cold Protease on Minced Tissue	MACS Enzyme on Crypts	Collagenase and DNase on Crypts	Cold Protease on Crypts	0.1X DSP	1% PFA
Contamination metrics
Empty Droplet Scaled Slope Sum	0.82	0.78	0.84	0.80	0.62	0.53	0.67
Inverted Max Secant Distance	0.78	0.83	0.86	0.79	0.68	0.65	0.67
Inverted Secant Line St.Dev.	0.44	0.45	0.46	0.44	0.40	0.40	0.40
Inverted AUC Percentage	0.70	0.76	0.80	0.72	0.58	0.54	0.56
Avg. Percent Counts Ambient	27.06	22.34	15.06	18.14	15.52	10.48	7.11
Standard metrics
Total Number of Cells	730.00	295.00	349.00	249.00	1019.67	2049.00	313.00
Avg. Percent Counts Mitochondria	9.86	5.06	3.18	5.83	4.03	2.05	0.57
Avg.Total Genes per Cell	990.96	1434.31	1989.21	2373.82	3682.52	3201.20	1685.39
Avg. Total Transcripts per Cell	1860.70	3220.45	4281.85	8155.20	12509.90	8209.73	4308.89
AmbiQuant
Overall score	0.69	0.70	0.71	0.67	0.57	0.52	0.56