Table 6

Real-time polymerase chain reaction analysis of 14 selected genes reveals good correlation with RNA-Seq results

Gene

RNA-Seq results

RT-PCR results


Differential expression

Significant log2 fold-change

Q value

Age

2-ΔCt log2 fold-change

P value

Mean Ct value, young

Mean Ct value, old


Young

Old


DKK1

Higher in old

-4.9

0.0006

0.0044 ± 0.006

0.0338 ± 0.20

-3.0

0.024

30.9

28.8

COL10

Higher in old

-1.4

0.03

0.0006 ± 0.0001

0.0013 ± 0.0009

-1.0

0.26

32.4

32.3

RUNX2

Lower in old

2.2

0.038

0.0093 ± 0.009

0.0034 ± 0.002

1.5

0.002

29

30.8

SRPX

Lower in old

1.6

0.009

0.0046 ± 0.005

0.0006 ± 0.0005

3.0

0.007

30

33.8

ACSL5

Lower in old

30.1

0.02

0.0155 ± 0.0002

0.0062 ± 0.005

1.3

0.09

29.5

29.6

IL7R

Lower in old

30.1

0.06

0.0005 ± 0.0002

0.0001 ± 0.0001

2.3

0.06

33.9

37

COL2A1

Lower in old

6.5

2.29 × 10-32

63.3246 ± 54.7

1.3165 ± 1.12

5.7

0.04

18.3

22.4

COL1A1

Lower in old

6.5

1.48 × 10-28

3.4815 ± 1.57

0.0278 ± 0.02

7.0

0.15

24.3

27.5

MMP1

Lower in old

1.6

0.006

0.7093 ± 0.21

0.4027 ± 0.14

0.8

0.05

23.1

24

MMP13

Lower in old

2

0.0003

0.2323 ± 0.15

0.044 ± 0.04

2.4

0.1

26.1

26.8

ADAMTS-4

Lower in old

1.9

0.0008

0.5121 ± 0.35

0.1345 ± 0.05

1.9

0.07

24

24.9

IL1β

Lower in old

6.2

8.91 × 10-10

0.0057 ± 0.005

0.0004 ± 0.0003

3.9

0.05

30.1

33.4

TNFα

No change

Not significant

1

0.0041 ± 0.004

0.001 ± 0.0003

2.1

0.28

31.1

32.1

TGFβ

No change

Not significant

1

1.2865 ± 0.23

2.3124 ± 1.24

-0.8

0.15

21.9

21.4


Values for real-time polymerase chain reaction (RT-PCR) are the mean ± standard deviation of relative expression levels normalised to expression of glyceraldehyde-3-phosphate dehydrogenase. Statistical significance was tested using Student's t test. Log2 fold-change of 2-ΔCt values is shown for comparison. Average threshold cycle (Ct) values for young and old donors are demonstrated to indicate robustness of expression. DKK1, dickkopf homolog 1; COL10, collagen type X; RUNX2, Runt-related transcription factor 2; SRPX, Sushi repeat-containing protein; ACSL5, acyl-CoA synthetase long-chain family member 5; IL7R, interleukin 7 receptor; COL2A1, collagen type II, alpha 1; COL1A1, collagen type I, alpha 1; MMP1, matrix metalloproteinase 1; MMP-13, matrix metalloproteinase 13; ADAMTS4, a disintegrin and metalloproteinase with thrombospondin motifs 4; IL-1β, interleukin 1 beta; TNFα, tumour necrosis factor alpha; TGFβ, transforming growth factor beta.

Peffers et al. Arthritis Research & Therapy 2013 15:R98   doi:10.1186/ar4278

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