. Author manuscript; available in PMC: 2022 Aug 13.

Published in final edited form as: Nat Protoc. 2022 Feb 4;17(2):445–475. doi: 10.1038/s41596-021-00651-w

Table 2. Example calculations of digestion efficiency.

Sample^a	Assay Set	Avg. CT	ΛCT (Cut-site − Fragment)	ΔΔCT (C1 − C2)	Digestion Efficiency^b
Control 1 (Undigested)	Fragment	21.211	-0.168	-2.706	84.76%
Control 1 (Undigested)	Cut-site	21.043	-0.168
Control 2 (Un-ligated)	Fragment	20.884	2.538
Control 2 (Un-ligated)	Cut-site	23.422	2.538

For low-input samples genomic DNA can be used instead of Control 1, and the 3C library in place of Control 2. Due to re-ligation a lower digestion efficiency is expected.

Efficiency = 100 x (1-2^ΔΔCT).