Table 1 Primer sets for COBRA and ChIP assay
From: Silencing of human T-cell leukemia virus type I gene transcription by epigenetic mechanisms
|  | Site in HTLV-Ia |  | Forward primer | Reverse primer | Anneal (°C) | Enzyme for COBRA |
|---|---|---|---|---|---|---|
COBRA | 620 | 1st | 5'-TTTGGAGTTTATTTAGATTTAG-3' | 5'-CCAATAATAAACRACCAACCC-3' | 45 | TaqI |
| Â | (5'-LTR) | 2nd | 5'-GTTTTGTTTGATTTTGTTTGT-3' | 5'-AAAAAAATTTAACCCATTACC-3' | 49 | Â |
| Â | 1753 | 1st | 5'-GGGAGTGTTAAAGATTTTTTTTGGG-3' | 5'-ACTCCAATAACCTACTTTCCC-3' | 55 | TaqI |
| Â | (gag) | 2nd | 5'-TTTATTTTTTAAGGTTTGGAGGAG-3' | 5'-TTAAAAATCCAAATCTAACAAACCC-3' | 55 | Â |
| Â | 2988 | 1st | 5'-GTTAAAAAGGTTAATGGAATTTGG-3' | 5'-CCTCTAAAAATAATAATAAATCCTC-3' | 52 | TaqI |
| Â | (pol) | 2nd | 5'-GGGTTTTTTGATTTGTTTAGTTTG-3' | 5'-AAACTTACTAAAAAAATATCATCC-3' | 51 | Â |
| Â | 4187 | 1st | 5'-GGGTGAAATTGTGTAGTTTTGTAGG-3' | 5'-CCTATTTTCAAACGAATCTACCTCC-3' | 57 | AccII |
| Â | (pol) | 2nd | 5'-GTGATTAGTAGGGTATTTGTGAGAG-3' | 5'-ATTATCACAAAAATCATTCCCCC-3' | 52 | Â |
| Â | 5151 | 1st | 5'-GGTATTATTTTAAGTTTTTTGG-3' | 5'-CTCCAATTATAAAAATACAACAAC-3' | 46 | TaqI |
| Â | (pol) | 2nd | 5'-GTTAGTGGAAAGGATTATAGGAGG-3' | 5'-AACTTACCCATAATATTAAAAATC-3' | 51 | Â |
| Â | 6113 | 1st | 5'-GGATTTATTGTTTTGATTTTTAG-3' | 5'-CTTTACATAATCCTCCTTACTCCC-3' | 51 | TaqI |
| Â | (env) | 2nd | 5'-GGATTTATTGTTTTGATTTTTAG-3' | 5'-CCCAAAACAAAAAATCAAAACC-3' | 53 | Â |
| Â | 7258 | 1st | 5'-GAGGTGGYGTTTTTTTTTTTGG-3' | 5'-CCTTAAAAATCTTAAAAATTCTC-3' | 47 | TaqI |
| Â | (pX) | 2nd | 5'-AAGGATAGTAAATYGTTAAGTATAG-3' | 5'-CCCAAATAATCTAATACTCTAAAC-3' | 50 | Â |
| Â | 8342 | 1st | 5'-YGATGGTAYGTTTATGATTTTYGGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 57 | TaqI |
| Â | (3'-LTR) | 2nd | 5'-YGATGGTAYGTTTATGATTTTYGGG-3' | 5'-AACTCCTACTAATTTATTAAACC-3' | 52 | Â |
| Â | 5'-LTRb | Â | 5'-GCTTTGCCTGACCCTGCTTGC-3' | 5'-AAGATTTGGCCCATTGCCTAGGG-3' | 63 | Â |
| Â | env | Â | 5'-TGCCAGCCTCTCCACTTGGCACG-3' | 5'-ATGGAGCCGGTAATCCCGCCAGC-3' | 64 | Â |
| Â | pX | Â | 5'-AAGGATAGCAAACCGTCAAGCACAG-3' | 5'-CCCAGGTGATCTGATGCTCTGGAC-3' | 63 | Â |
| Â | 3'-LTR | Â | 5'-CCCCTCATTTCTACTCTCACACGGC-3' | 5'-TGGGTGGTTCTTGGTGGCTTCCC-3' | 64 | Â |