Table 2 Primers and TaqMan™ probes used for 3C analysis
Primers for MboI 3C analysis | |
HS4 (anchor) | GAGAATCGGGTGCAGGCTT |
HS4 -|- HS3 | GCGTGGATAGAAGTAAACTGGAA |
HS3 | GCAGTCCCAGGTTGCACAA |
HS2 (anchor) | CACCGTCAGCATACATTGCT |
HS2 -|- HS1 | CAGGACCACCGTTACCCAT |
HS1 | TCAGGAACCGTGGGTGTGT |
HS1 -|- Rho | ACAACTCCAAGGGATGAAGC |
Rho (anchor) | AGGGAGACTACGAATGCTGC |
Rho -|- betaH | AATGGAAAGGTTCTGTCTCAGC |
BetaH | CTGAGCCCCACCCTGATG |
BetaH -|- BetaA | ACTATGTCCATCCCAGCTCCA |
BetaA (anchor) | AGCCCCACTGCCATCCTT |
BetaA -|- Beta/eps enh | TCACGGAGCACCTACAACCA |
Beta/eps enh (anchor) | CTATCAAGACTTGCACAGACCTT |
Beta/eps enh -|- Epsilon | AGTGATTCTATGGAGGAAGGCA |
Epsilon (anchor) | GCGACAAGTTGCACGTGG |
3′HS (anchor) | GGGCATTTCTACAGAGAGCAA |
Downstream to 3′HS | CCACATCTGCCAAGAGCCT |
ERCC3 test | CAAATCTGACAGCCGCTTAGA |
ERCC3 (anchor) | CTCGATGAAGTACATACTATTCCTG |
Primers for NlaIII 3C analysis | |
HS4 | GTGGATTGAAGGATGCTGAG |
HS4 -|- HS3 | CCAAAGGACCCCAGGACTA |
HS3 | TGACACAGCACAAAAGTGAGC |
HS3 -|- HS2 | AGCAATGTATGCTGACGGTG |
HS2 | AAATACATCCCATCCTGGTGTTC |
HS2 -|- HS1 | CAGGAAAAGCCTTACTTCAAATG |
HS1 | CCGCTGCTCAGTGTCACAC |
HS1 -|- Rho | CGAAGTAGGGAACCTCAACA |
Rho | AGGAGGGGAGTAAAAGGGAG |
BetaH | CCCTGAACGATGAGTAGGAAGT |
BetaA | CAGCTCTGCAGCTCTATACCG |
Beta/eps enh | TTAATCCTCCCTGGATCATTTC |
Beta/eps enh -|- Epsilon | GCTCTGCTTACATTCACATCCA |
Epsilon (anchor) | AGCGCTGCCCTACCAGAC |
Epsilon -|- 3′HS | AGCAGCCTGCAGAGGGAT |
3′HS | GGGCATTTCTACAGAGAGCAA |
ERCC3 test | CAAATCTGACAGCCGCTTAGA |
ERCC3 (anchor) | CTCGATGAAGTACATACTATTCCTG |
TaqMan™ probes for MboI 3C analysis | |
HS4 | FAM-ATTCCCTGTCC(T-BHQ1)GTCCCACAGCTGT-PO4 |
HS2 | FAM-AATTTGTGA(T-BHQ1)GGACTTCAGGCCCAT-PO4 |
Rho | FAM-AAAGGAGCTGAC(T-BHQ1)CATGCTAGCCCAG-PO4 |
BetaA | FAM-TTTGCCTCC(T-BHQ1)TTGGGAACCTCTCC-PO4 |
Beta/eps enh | FAM-CAGTTCTCCGAG(T-BHQ1)CTGACTTTGGAGTCT-PO4 |
Epsilon | FAM-TTTGCCTCC(T-BHQ1)TTGGGAACCTCTCC-PO4 |
3′HS | FAM-CAGTTCTCCGAG(T-BHQ1)CTGACTTTGGAGTCT-PO4 |
ERCC3 | FAM-TGGAGTGGCT(T-BHQ1)AAAAGTCGAGAGTGG-PO4 |
TaqMan™ probes for NlaIII 3C analysis | |
HS2 | FAM-AAGTG(T-BHQ1)CCCAGCTCCTGTTCTCCCAC-PO4 |
Epsilon | FAM-CCTTTCTC(T-BHQ1)GAAAAGGGGCCCAGGT-PO4 |
ERCC3 | FAM-TGGAGTGGCT(T-BHQ1)AAAAGTCGAGAGTGG-PO4 |