Table II.
Bisulfite modified primers for PCR and MS-SNuPE assay
| Name | Position | 5′-3′ Sequencea |
|---|---|---|
| COL1A2 primers | ||
| Forward primer (FP) | α2(1) Promoter −65 to −37 | GGAGGTATTTTAGGTTAGGGAAATTTTTG |
| Reverse primer (RP) | α2(I) First exon +121 to +151 | CACAAAACTAAACATATCTAACACTTAAA |
| +7 primer (SNuPE) | α2(I) Transcription start site −17 to +6 | GGGATTTGTTATTTTAAGTATTA |
| Control primer | α2(I) Promoter −59 to −43 | ATTTTAGGTAGGGAAA |
| COL1A1 primers | ||
| Forward primer (FP) | α1(1) Promoter −15 to −98 | AATTAATCTCAACAAACC |
| Reverse primer (RP) | α1(1) First exon +78 to +96 | ATTTTTTGTGGTTGGGGAG |
| +6 primer (SNuPE) | α1(1) Transcription start site −14 to +5 | AAACAAAACTACTAACCAA |
a
The PCR and MS-SNuPE primers are the predicted bisulfite converted collagen bases based on COL1A2 sequences in the GenBank (accession number AF004877). The PCR primers have been chosen from regions that do not contain any methylation sites. The region amplified by these primers contained a % GC of 56% and a CG:GC ratio of 0.55.