Table 2 Primer Sequences and Conditions for qRT-PCR, Bisulfite sequencing and MSP Analysis
From: Promoter methylation correlates with reduced NDRG2expression in advanced colon tumour
Gene symbol | RefSeq mRNA | Primer Forward (5'-->3') | Primer Reverse (5'-->3') | Size (bp) | AT†(°C) |
|---|---|---|---|---|---|
| Â | Â | Quantitative Real Time PCR (qPCR) assay | Â | Â | Â |
ABCA8 | NM_007168 | CCATCATGGTATCTGGGAGGTT | GCAGGTAATCTTTGCCAAATTTG | 77 | 60 |
AQP8 | AB013456 | CACGGGCTGGCTTTGG | CCAGTACGGGAGGAGCATCA | 128 | 60 |
CLCA4 | NM_012128 | CAAAATGGCCTATCTCAGTATTCCA | TCGCTTTGGCTTGAAGATTGT | 68 | 60 |
HPGD1 | NM_000860 | GCATGGCATAGTTGGATTCACA | AAGCCTGGACAAATGGCATT | 83 | 60 |
PRDX6 | NM_004905 | GCCCTTTCAATAGACAGTGTTGAG | ATCGATGATGGGAAAAGGTAACTT | 104 | 60 |
SLC26A3 | NM_000111 | ATCGTTGGAACTGATGATGACTTC | CAGCATCATGGATTGTTAAGAAAAA | 90 | 60 |
STX12 | NM_177424 | AAGAAAGAGAAACGGCAATTCG | TCATGGCCAAATCTTTAAATATCTGA | 75 | 60 |
CSE1L | NM_001316 | CGGTTCAAACACAATAGCAAGTG | GGATGCAATCAGCTTCTGAAAGA | 78 | 60 |
HSPH1 | NM_00664 | AACAAAATCCCAGATGCTGACA | ACCTTTATTTTGGGCTTTTTAGCTT | 79 | 60 |
NEBL1 | HSY1624 | ATCCATGAGATCAATGCAGCAT | CATCCTGGGCACTGTAATCGT | 73 | 60 |
RFC3 | NM_002915 | CTGAGGGAGACTGCAAATGCT | ACAGCCTTCCACGAACTTCAA | 72 | 60 |
SLC12A2 | NM_001046 | AAGGAACATTCAAGCACAGCTAATATT | TGCCATGTAGAGAGCACTAGACACA | 86 | 60 |
SOX9 | NM_000346 | ACGCCGAGCTCAGCAAGA | CACGAAGGGCCGCTTCT | 70 | 60 |
GTF2IRD1 | ENST00000265755 | AATCTGCAATGATGCCAAGGT | CCGAGACCCGCTTTCTCTT | 70 | 60 |
MXI1 | NM_005962 | CGGCACACAACACTTGGTTT | GGCTTTTTCTTTCAGCTTCTTCA | 75 | 60 |
NR3C2 | NM_000901 | TTCATTCTCAGTACCAATAAAGCAAGA | GGTTTACTGTTGGATTCCCTTTAAAA | 82 | 60 |
SGK1 | NM_005627 | AGGAGCCTGAGCTTATGAATGC | GACGACGGGCCAAGGTT | 75 | 60 |
NDRG2 | NM_201535 | CTGACCGAGGCCTTCAAGTACT | GGCGAGTCATGCAGGATGA | 66 | 60 |
TPX2 | NM_012112 | AGCCCTTTGTTCCCAAGAAAG | CCAGCTGAAAAGGTTCCTGAA | 80 | 60 |
UBE2C | NM_181799 | TGGAGCTTACTCTGCAACTGTTTC | CCAAATGCCAGAACCCAACATTGATAGTCC | 74 | 60 |
CCNB1 | NM_031966 | CCTGGCTAAGAATGTAGTCATGGTAA | GCATGCTTCGATGTGGCATA | 83 | 60 |
SCNN1B | ENST00000343070 | CATTGAAGAATCAGCAGCCAATA | CCCATCCAGAAGCCAAACTG | 74 | 60 |
FOXM1 | U74613 | AGCAAGCGAGTCCGCATT | CTGCAGAAGAAAGAGGAGCTATCC | 68 | 60 |
SGK2 | NM_016276 | ACATCATTTACAGGGATCTGAAACC | TCCTTGCAGAGGCCAAAATC | 87 | 60 |
| Â | Â | Bisulfite Sequencing Analysis (BSA) | Â | Â | Â |
NDRG2 | Â | TTTTCGAGGGGTATAAGGAGAGTTTATTTT | CCAAAAACTCTAACTCCTAAATAAACA | 320 | 53 |
CSE1L | Â | GTTTGGAATTTTAGTATTTTGGGAG | CTCTAACCATACCAACAAACTTCAC | 285 | 60 |
HSP1 | Â | GGAGAGGGTTTGGGTATGTAA | CAAAAAAATAAAATAAACCTAAAAAAC | 194 | 56 |
PRDX6 | Â | TATTTTTTTGTAGGGAGTTGGT | TAACATCCTTCAAACACTATAAACC | 279 | 56 |
SOX9 | Â | TTTTTATTGATTTTTTTTGTAAAAG | ATACCAAAATTTTAATACCTTCTCC | 388 | 53 |
| Â | Â | Methylation-Specific PCR (MSP) assay ? | Â | Â | Â |
NDRG2_UnM | Â | AGAGGTATTAGGATTTTGGGTATGA | CCACTAAAAAAACAAAAATCTCACC | 125 | 55 |
NDRG2_M | Â | AGAGGTATTAGGATTTTGGGTACG | GCTAAAAAAACGAAAATCTCGC | 123 | 55 |
NDRG2_UnM_2 | Â | GGTAAATTTATTTGGGTATTGA | CAAAAACAAAATTAACCCTACAAA | 210 | 54 |
NDRG2_M_2 | Â | TAGTGGTAAATTTATTCGGGTATCG | CAAAAACGAAATTAACCCTACGA | 214 | 62 |
p16-UnM | Â | TTATTAGAGGGTGGGGTGGATTGT | CAACCCCAAACCCACAACCATAA | 151 | 65 |
p16-M | Â | TTATTAGAGGGTGGGGCGGATCGC | GACCCCCGAACCGCGAACCGTAA | 150 | 68 |
APC-UnM | Â | GTGTTTTATTGTGGAGTGTGGGTT | CCAATCAACAAACTCCCAACAA | 108 | 63 |
APC-M | Â | TATTGCGGAGTGCGGGTC | ACCACCTCATCATAACTACCCACA | 98 | 63 |
MLH1-UnM | Â | TTTTGATGTAGATGTTTTATTAGGTTGT | ACCACCTCATCATAACTACCCACA | 124 | 60 |
MLH1-M | Â | ACGTAGACGTTTTATTAGGGTCGC | CCTCATCGTAACTACCCGCG | 115 | 60 |