Table 1 Primer sequences, annealing temperatures, and amplicon information for the MS-HRM and SMART-MSP assays (UCSC Genome Browser, August 2008).
Gene | Primer sequences (CpG sites underlined and converted Cs as capital Ts or As). (5'→ 3'). | Annealing temperature | Amplicon size | CpGs/non-CpG-Cs between the primers | Spanned region(bp) |
|---|---|---|---|---|---|
CDKN2A (MS-HRM) | F-ggagTTttcggTtgaTtggTtggTT R-aAcaAcgcccgcacctcctcta | 64°C | 69 bp | 5/3 | 21964733-21964800 of Chr. 9 |
RARB (MS-HRM) | F-cgagTtgtttgaggaTtgggatgT R-aatAcgttccgAatcctacccc | 64°C | 89 bp | 7/5 | 25444840-25444928 of Chr. 3 |
CDKN2A (SMART-MSP) | F-gTtgaTtggTtggTTacgTcgc R-ctcctctacccgaccccgA | 64°C | 45 bp | 0/1 | 21964746-21964790 of Chr. 9 |
RARB (SMART-MSP) | F-gggatgTcgagaacgcgagc R-cgAtAcccaAacaaaccctActcg | 64°C | 48 bp | 0/1 | 25444857-25444904 of Chr. 3 |
ALU control (SMART-MSP) | F-ggttaggtatagtggtttatatttgtaattttagta R-attaactaaactaatcttaaactcctaacctca | 62°C | 98 bp | N/A | Consensus seq., See ref [23]. |