Table 2.
Comparison of meSDC2 LTE-qMSP with meSDC2-qMSP
| Description | meSDC2 LTE-qMSP | meSDC2-qMSP |
|---|---|---|
|
SDC2
Primer sequencesa |
5′-GT
A
G
A
A
A
T
T
A
A
T
A
A
G
T
G
A
G
A
G
G
G
C-3′ 5′-AAAGATTCGGCGACCACCGAACG A C T C A A A C T CG A A A A C T CG-3′ |
F: 5′-TAGAAATTAATAAGTGAGAGGGCGT-3′ R: 5′-GACTCAAACTCGAAAACTCGAA-3′ |
| SDC2 probea | 5′-FAM-TTCGGGGCGTAGTTGCGGGCGG-3′ | 5′-FAM-AGTAGGCGTAGGAGGAGGAAGCGA-3′ |
| SDC2 amplicon size | 124 bp | 121 bp |
| Real time PCR reagents | AptaTaq DNA Master, 5X | Rotor-Gene Probe PCR Kit |
| Thermal cycling condition | LTE: 95 °C 5 min; 95 °C 15 s, 60 °C 1 min, 35 cycles; heating and cooling rates were 15 and 20 °C/s. qMSP: 95 °C 5 min; 95 °C 15 s, 60 °C 1 min, 40 cycles; heating and cooling rates were 15 and 20 °C/s. |
qMSP: 95 °C 5 min; 95 °C 10 s, 62 °C 15 s, 72 °C 20 s; 40 cycles; heating and cooling rates were 15 and 20 °C/s. |
| Control gene | COL2A1 | ACTB |
| Primer sequencesa | 5′-GTAATGTTAGGAGTATTTTGTGGITA-3′ 5′-AAAGATTCGGCGACCACCGACTAICCCAAA AAAACCCAATCCTA-3′ |
F: 5′-TGGTGATGGAGGAGGTTTAGTAAGT-3′ R: 5′-AACCAATAAAACCTACTCCTCCCTT AA-3′ |
| COL2A1 probea | 5′-Cy5-AGAAGAAGGGAGGGGTGTTAGGAGAGG-3′ | 5′-TET-ACCACCACCCAACACACAATAACAAACA CA-3′ |
| COL2A1 amplicon size | 86 bp | 133 bp |
Bold identical nucleotide sequences with meSDC2-qMSP assay, italics universal sequence, I inosine nucleotide, F and R indicate forward and reverse primers, respectively
aCpG dinucleotide sites are underlined