Table 2 Primer sets and annealing temperatures for genome specific PCR
From: Silencing of human T-cell leukemia virus type I gene transcription by epigenetic mechanisms
|  | Case | Locus |  | Forward primer | Reverse primer | Anneal (°C) |
|---|---|---|---|---|---|---|
Primers for case | Acute ATL 1 | 5q11.1 | 1st | 5'-TTTGGAGAGGGAATTTTATATTG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 55 |
| Â | Â | Â | 2nd | 5'-GGAGTGTAGAGATGTAGTTTTGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 50 |
| Â | Acute ATL 2 | 8p23.1 | 1st | 5'-GAGAAATTTGTGTTGATTTTATTAG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 47 |
| Â | Â | Â | 2nd | 5'-TTAGTGGTAGATTAAGTTAAAG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 45 |
| Â | Acute ATL 3 | 1q31.1 | 1st | 5'-GGTAGAAATTATAGGTTTTTGTAGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 51 |
| Â | Â | Â | 2nd | 5'-GTTATTTGTGAAGTAAGATGTTTTG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 53 |
| Â | Acute ATL 21 | 15q24.3 | 1st | 5'-GAGGTGGATTTTTATTTTATTG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 52 |
| Â | Â | Â | 2nd | 5'-GGTTTTTGATTATATTTGGGGAG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 54 |
| Â | Acute ATL 22 | 19q13.11 | 1st | 5'-GTTAGTTGTTAGAGAGTTTTTTGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 52 |
| Â | Â | Â | 2nd | 5'-AAGATTATTTAGTTTTTTGGGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 54 |
| Â | Chronic ATL 1 | 1p22.1 | 1st | 5'-GGGTTTGAAGTTTTTTTTGTAGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' | 53 |
| Â | Â | Â | 2nd | 5'-AAGATTATTTAGTTTTTTGGGG-3' | 5'-ACCCCCTCCTAAACTATCTCC-3' (5'-LTR U3) | 50 |
Primers for human genome | Â | 5q11.1 | 1st | 5'-TTTGGAGAGGGAATTTTATATTG-3' | 5'-CCCAAACTAATCTTCAACTCC-3' | 52 |
| Â | Â | Â | 2nd | 5'-GGAGTGTAGAGATGTAGTTTTGG-3' | 5'-CCACCATAAAAAACCCTCCC-3' | 54 |
| Â | Â | 8p23.1 | 1st | 5'-GAGAAATTTGTGTTGATTTTATTAG-3' | 5'-AATATCACTATAACAATAACCAC-3' | 46 |
| Â | Â | Â | 2nd | 5'-TTAGTGGTAGATTAAGTTAAAG-3' | 5'-CTCTCAACAAATTCCATCTTTCC-3' | 49 |
| Â | Â | 1q31.1 | 1st | 5'-GGTAGAAATTATAGGTTTTTGTAGG-3' | 5'-CACCATTAAACAAACTAAATTCTC-3' | 51 |
| Â | Â | Â | 2nd | 5'-GTTATTTGTGAAGTAAGATGTTTTG-3' | 5'-CACATAAAAAAACCCACACAATC-3' | 53 |
| Â | Â | 15q24.3 | 1st | 5'-GAGGTGGATTTTTATTTTATTG-3' | 5'-ATCTACCTAAAAAACCCACCC-3' | 52 |
| Â | Â | Â | 2nd | 5'-GGTTTTTGATTATATTTGGGGAG-3' | 5'-AAAAACCCACCCAAACAAACC-3' | 57 |
| Â | Â | 19q13.11 | 1st | 5'-GTTAGTTGTTAGAGAGTTTTTTGG-3' | 5'-CAACTCCCTAAACCCTCCTCC-3' | 52 |
| Â | Â | Â | 2nd | 5'-GTTTTTTGGTTAAGGTTATGGG-3' | 5'-CTCCTACCACGAACCTACTCC-3' | 54 |
| Â | Â | 1p22.1 | 1st | 5'-GGGTTTGAAGTTTTTTTTGTAGG-3' | 5'-CAACAAAAACAATAAACAAAACC-3' | 54 |
| Â | Â | Â | 2nd | 5'-AAGATTATTTAGTTTTTTGGGG-3' | 5'-CTTTACACCAATAAATTTAATACC-3' | 50 |