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Table 2 Primers, product length and specific amplification conditions for qPCR

From: In vitromodel for the analysis of synovial fibroblast-mediated degradation of intact cartilage

Gene

Primer forward

Primer reverse

Accession number

T annealing

Melting T product

Human/bovine Aldolase A

5'-TCATCCTCTTCCATGAGACACTCTA-3'

5'ATTCTGCTGGCAGATACTGGCATAA-3'

[GenBank: NM_000034]

58°C

88°C

Human MMP-1

5'-GACCTGGAGGAAATCTTGC-3'

5'-GTTAGCTTACTGTCACACGC-3'

[GenBank: NM_002421]

58°C

86°C

Human MMP-3

5'-CTCACAGACCTGACTCGGTT-3'

5'-CACGCCTGAAGGAAGAGATG-3'

[GenBank: NM_002422]

58°C

81°C

Human IL-6

5'-ATGAACTCCTTCTCCACAAGCG-3'

5'-CTCCTTTCTCAGGGCTGAG-3'

[GenBank: NM_000600]

60°C

86°C

Human IL-8

5'-GCCAAGAGAATATCCGAACT-3'

5'-AGGCACAGTGGAACAAGGACTTGT-3'

[GenBank: NM_000584]

60°C

78°C

Bovine MMP-1

5'-CAAGAGCAGATGTGGACCAA-3'

5'-CTGGTTGAAAAGCATGAGCA-3'

[GenBank: NM_174112]

61°C

83°C

Bovine MMP-3

5'-CTGGTGTCCAGAAGGTGGAT-3'

5'-TAGGCGCCCTTGAAGAAGTA-3'

[GenBank: AB043995]

61°C

83°C

Bovine IL-6

5'-ATGAACTCCCGCTTCACAAG-3'

5'-CCTTGCTGCTTTCACACTCA-3'

[GenBank: NM_173923]

61°C

83°C

Bovine IL-8

5'-TGCTCTCTGCAGCTCTGTGT-3'

5'-CAGACCTCGTTTCCATTGGT-3'

[GenBank: NM_173925]

64°C

81°C

Bovine Col II (α 1 chain)

5'-CATCTGGTTTGGAGAAACCATC-3'

5'-GCCCAGTTCAGGTCTCTTAG-3'

[GenBank: NM_001001135]

61°C

83°C

Bovine COMP

5'-ATGCGGACAAGGTGGTAGAC-3'

5'-TCTCCATACCCTGGTTGAGC-3'

[GenBank: X74326]

61°C

87°C

  1. General amplification protocol (40 cycles): initial denaturation for two minutes at 95°C; denaturation for 15 seconds at 95°C, specific primer annealing temperature (see table) for 15 seconds, amplification at 68°C for 20 seconds, additional heating step to 5°C below the melting temperature of the PCR product (see table). General melting curve protocol (one cycle): denaturation for one second at 95°C; cooling to 5°C above the primer annealing temperature (holding for 10 seconds); heating to 95°C (0.1°C/second); final cooling for five minutes at 40°C.
  2. Col = collagen; COMP = cartilage oligomeric matrix protein; IL = interleukin; MMP = matrix metalloproteinase; qPCR = quantitative polymerase chain reaction.