. 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 1. 3C digestion efficiency qPCR primers.

Assay Set	Sequence	Site	DpnII	NlaIII
Homo sapiens (hg38)
Hs 1 forward	5’-GTCAGAAATAACAGGAAACCCAAA-3’	chr22:46,257,116-46,257,137	Cut-site	Cut-site
Hs 1 reverse	5’-TTACTTGTCGAACCCAGAAGAC-3’	chr22:46,257,190-46,257,212	Cut-site	Cut-site
Hs 2 forward	5’-GAGAATGGCCACATACAAGTAGA-3’	chr22:46,257,407-46,257,429	Fragment	Fragment
Hs 2 reverse	5’-GGAGTTGTCAACACAAGCATATC-3’	chr22:46,257,480-46,257,502	Fragment	Fragment
Mus musculus (mm9)
Mm 1 forward	5’-GGAGAAAGAAGGCTGGTGTTAT-3’	chr15:85,650,603-85,650,624	Cut-site	Fragment
Mm 1 reverse	5’-TATCTGAGTTGGACAGCATTGG-3’	chr15:85,650,686-85,650,707	Cut-site	Fragment
Mm 2 forward	5’-TTATCTTGCATTTGCCAACTCG-3’	chr15:85,650,801-85,650,822	Fragment	Cut-site
Mm 2 reverse	5’-TGGGTTTCCCTGATTCTGAAA-3’	chr15:85,650,880-85,650,900	Fragment	Cut-site
Drosophila melanogaster (dm6)
Dm 1 forward	5’-CAGGCCAACACACATTGTATC-3’	chr3R:23,023,063-23,023,083	Cut-site	NA
Dm 1 reverse	5’-CGGCAGGCAAATCGAATAAA-3’	chr3R:23,023,146-23,023,165	Cut-site
Dm 2 forward	5’-TGTTAGTCCCTGCCTCTGTA-3’	chr3R:23,023,278-23,023,297	Fragment
Dm 2 reverse	5’-AAGTAACAGCAGCTGGAATAGG-3’	chr3R:23,023,358-23,023,379	Fragment