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Table 1 Primer sequences, annealing temperatures, and amplicon information for the MS-HRM and SMART-MSP assays (UCSC Genome Browser, August 2008).

From: Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM

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].