Primers and amplification conditions for ChIP and RT-PCR
Primer set . | Primer sequence, 5′-3′ . | Annealing temperature, °C . | No. cycles . | Product, no. bp's . |
|---|---|---|---|---|
| VH-3 (B-JAB), ChIP | F: GGCCCTCCCTCTACTGATGAAAACCA | 60 | 35 | 498 |
| R: ATTGTAGCCATCTCCCGTGCCCTCTT | ||||
| VH-1 (L1236), ChIP | F: TGGGACATCTATCTTCTTTCTCAACCTC | 63 | 35 | 636 |
| R: ACTGCGCCACCTGCCACCTCTC | ||||
| VH-3 (KM-H2), ChIP | F: GTTAATCAAGGCACAATCATA | 54.8 | 35 | 731 |
| R: GCACCCCCTCGCACAGAAATAAA | ||||
| VH-4 (Namalwa), ChIP | F: CCTCCCTCATCCCTTTTCACCTCT | 62 | 35 | 622 |
| R: GTCGCCACCACTCCAAAAATCGTA | ||||
| VH-5 (L428), ChIP | F: GCAACTATGCAAATGCAAGTGGGG | 63 | 35 | 500 |
| R: AGATAGGCAGTGGAGACGGATTTGTC | ||||
| Internal enhancer, ChIP | F: AGGCCAGATCTGAAAGTGCT | 57 | 35 | 320 |
| R: TAATGCTCTGAGGTATCGAAAAAGTA | ||||
| Cα1-enhancer, ChIP | F: GGGGGAGGGGGCGGGAGAAT | 60 | 35 | 278 |
| R: GGGGCAAGCTGGTGAGGAAAGTGG | ||||
| Cα2-enhancer, ChIP | F: CCAAGTGGGCCTGTCCTG | 60 | 35 | 408 |
| R: GGGCTCTGATCTGTTTCTCCTT | ||||
| Cα2-enhancer KM-H2, ChIP | F: GCCTGGCCACGCTGTTG | 58.7 | 35 | 296 |
| R: AGGGCTCTGATCTGTTTCTCC | ||||
| H2B histone promoter, ChIP | F: GGGCGCGAAAAAGAAGACGTGTTGTTG | 65 | 35 | 284 |
| R: GAGGTGATGGTCGAGCGCTTGTTGTAA | ||||
| Involucrin promoter, ChIP | F: TGAGCATGGCATTCCTGAGA | 54.8 | 35 | 423 |
| R: GGCATCCTACTGTTTTGTGACCT | ||||
| KMH2 leader, RT-PCR | F: TGGGCTGACCTGGGTTTTCCTCGTT | 59.3 | 35 | 494/392 |
| R: CCTTGGCCCCAGTGGTCAGATA | ||||
| L428 leader, RT-PCR | F: AACCGCCATCCTCGCCCTCCTC | 61.0 | 35 | 444/360 |
| R: CCCCATCATCTGACTATGTCTCCCACAG | ||||
| L1236 leader, RT-PCR | F: CCTGGAGGGTCTTCTGCT | 55.6 | 35 | 410/324 |
| R: ACGGCCGTGTCCTCAAA | ||||
| PBDG30 | F: AGCTGCAGAGAAAGTTCCC | 60 | 30 | 437 |
| R: GTTACGAGCAGTGATGCC |
Primer set . | Primer sequence, 5′-3′ . | Annealing temperature, °C . | No. cycles . | Product, no. bp's . |
|---|---|---|---|---|
| VH-3 (B-JAB), ChIP | F: GGCCCTCCCTCTACTGATGAAAACCA | 60 | 35 | 498 |
| R: ATTGTAGCCATCTCCCGTGCCCTCTT | ||||
| VH-1 (L1236), ChIP | F: TGGGACATCTATCTTCTTTCTCAACCTC | 63 | 35 | 636 |
| R: ACTGCGCCACCTGCCACCTCTC | ||||
| VH-3 (KM-H2), ChIP | F: GTTAATCAAGGCACAATCATA | 54.8 | 35 | 731 |
| R: GCACCCCCTCGCACAGAAATAAA | ||||
| VH-4 (Namalwa), ChIP | F: CCTCCCTCATCCCTTTTCACCTCT | 62 | 35 | 622 |
| R: GTCGCCACCACTCCAAAAATCGTA | ||||
| VH-5 (L428), ChIP | F: GCAACTATGCAAATGCAAGTGGGG | 63 | 35 | 500 |
| R: AGATAGGCAGTGGAGACGGATTTGTC | ||||
| Internal enhancer, ChIP | F: AGGCCAGATCTGAAAGTGCT | 57 | 35 | 320 |
| R: TAATGCTCTGAGGTATCGAAAAAGTA | ||||
| Cα1-enhancer, ChIP | F: GGGGGAGGGGGCGGGAGAAT | 60 | 35 | 278 |
| R: GGGGCAAGCTGGTGAGGAAAGTGG | ||||
| Cα2-enhancer, ChIP | F: CCAAGTGGGCCTGTCCTG | 60 | 35 | 408 |
| R: GGGCTCTGATCTGTTTCTCCTT | ||||
| Cα2-enhancer KM-H2, ChIP | F: GCCTGGCCACGCTGTTG | 58.7 | 35 | 296 |
| R: AGGGCTCTGATCTGTTTCTCC | ||||
| H2B histone promoter, ChIP | F: GGGCGCGAAAAAGAAGACGTGTTGTTG | 65 | 35 | 284 |
| R: GAGGTGATGGTCGAGCGCTTGTTGTAA | ||||
| Involucrin promoter, ChIP | F: TGAGCATGGCATTCCTGAGA | 54.8 | 35 | 423 |
| R: GGCATCCTACTGTTTTGTGACCT | ||||
| KMH2 leader, RT-PCR | F: TGGGCTGACCTGGGTTTTCCTCGTT | 59.3 | 35 | 494/392 |
| R: CCTTGGCCCCAGTGGTCAGATA | ||||
| L428 leader, RT-PCR | F: AACCGCCATCCTCGCCCTCCTC | 61.0 | 35 | 444/360 |
| R: CCCCATCATCTGACTATGTCTCCCACAG | ||||
| L1236 leader, RT-PCR | F: CCTGGAGGGTCTTCTGCT | 55.6 | 35 | 410/324 |
| R: ACGGCCGTGTCCTCAAA | ||||
| PBDG30 | F: AGCTGCAGAGAAAGTTCCC | 60 | 30 | 437 |
| R: GTTACGAGCAGTGATGCC |
F indicates forward; R, reverse; and PBDG, porphobilinogen deaminase.