MSP and bisulphite sequencing primers for the SDHD, SDHB, and VHL promoters
Gene | Type of primer | Primer sequence (5′–3′) | Untreated DNA (5′–3′) | Annealing temperature |
---|---|---|---|---|
Y, C+T; R, G+A; U, primers for unmethylated DNA; M, primers for methylated DNA. | ||||
Primer sequences are given as forward and reverse for each set. | ||||
MSP | ||||
SDHB | U | TAAATGGGTATGTGTTGTTATTGT | CAAATGGGCATGCGCCGCTACTGC | 60°C |
AACCACATACAAACAACCAAATAA | AGCCGCGTACGAGCAACCAAGTGG | |||
M | TGGGTATGCGTCGTTATTGC | TGGGCATGCGCCGCTACTGC | ||
CGCGTACGAACAACCAAATAA | CGCGTACGAGCAACCAAGTGG | |||
SDHD | U | TGATAGTTGTGTTTGTGTATGTGT | CGACAGCTGTGTTTGCGCATGCGC | 60°C |
AAACCACCATCTCATTCCTAAA | GAACCGCCATCTCGTTCCTGAG | |||
M | AGTTGTGTTTGCGTATGCGC | AGCTGTGTTTGCGCATGCGC | ||
AACCGCCATCTCGTTCCTAA | AACCGCCATCTCGTTCCTGA | |||
VHL | U | GTTGGAGGATTTTTTTGTGTATGT | GCTGGAGGATCCTTCTGCGCACGC | 60°C |
CCCAAACCAAACACCACAAA | CCCGGATCCCGCGGCGTCC | |||
M | TGGAGGATTTTTTTGCGTACGC | TGGAGGATCCTTCTGCGCACGC | ||
GAACCGAACGCCGCGAA | CGGATCCCGCGGCGTCC | |||
Bisulphite | ||||
SDHB | GGAATAAAGAGGTTGAAATYGGG | GGAATAAAGAGGTTGAAATCGGGG | 60°C | |
AACCTACATCCACTAAAAACCCAC | AGCCTACATCCACTGAGGACCCAC | |||
SDHD | 1st set | TGAGGGGAATGGGATGTAGT | TGAGGGGAATGGGATGCAGC | 60°C |
CTAAAAACTCAAAATCATCCACCAA | CTGAGGGCTCAAGGTCATCCACCAA | |||
2nd set | AGGGGATGGAAGTGAGGATTTA | AGGGGATGGAAGTGAGGACTCA | 59°C | |
AACAAACTCCTAACCCTCTTTC | GGCAAGCTCCTAACCCTCTTTC | |||
VHL | 1st set | TAGTGGAAATATAGTAAYGAGTTGG | TAGTGGAAATATAGTAACGAGTTGG | 57°C |
CCCTCCRAAACATTCCCTC | CCCTCCGAAACATTCCCTC | |||
2nd set | TAYGGTGTTGGAGGATTTTTTTG | TACGGTGCTGGAGGATCCTTCTG | 57°C | |
TCTTCTTCAAAACCRTACTCTTC | TCTTCTTCAGGGCCGTACTCTTC |