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Table 6 Verification of microarray results by Real-time PCR.

From: Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

  

Real time PCR IR vs OUT

Affymetrix microarray

Gene

Day

IR*

OUT*

SED**

Fold Change

P-value

Fold Change

P-value

FKBP5

5

5.56 ± 0.76

4.77 ± 0.72

0.42

-1.73

0.092

-1.56

0.014

IRF7

5

6.12 ± 1.43

7.70 ± 1.04

0.72

2.99

0.056

5.00

0.003

IRP6

5

5.62 ± 2.97

8.75 ± 1.54

1.37

8.71

0.054

8.28

0.008

MT1J

5

2.31 ± 3.61

7.78 ± 1.88

1.66

44.33

0.012

28.70

0.002

MX

5

6.20 ± 2.35

8.08 ± 0.45

0.98

3.66

0.110

4.67

0.017

PDK4

5

9.30 ± 1.13

8.39 ± 0.38

0.49

-1.88

0.111

-3.19

0.005

SQLE

5

5.85 ± 1.51

7.59 ± 1.44

0.85

3.34

0.069

5.69

0.044

CCL8

28

8.28 ± 0.87

10.29 ± 1.29

0.68

4.04

0.021

4.41

0.000

CXCL12

28

4.44 ± 0.23

5.15 ± 0.27

0.14

1.63

0.001

1.83

0.003

CXCL9

28

4.91 ± 1.30

7.37 ± 2.36

1.10

5.52

0.057

6.28

0.007

IRF7

28

5.21 ± 1.55

6.20 ± 0.70

0.69

1.99

0.196

3.56

0.006

MT1J

28

3.33 ± 2.10

6.58 ± 1.58

1.07

9.49

0.014

13.01

0.001

PDK4

28

9.75 ± 0.66

7.61 ± 0.78

0.42

-4.43

0.000

-11.62

0.000

SQLE

28

5.14 ± 1.12

7.27 ± 2.04

0.95

4.38

0.056

6.34

0.001

TFRC

28

5.78 ± 1.38

7.62 ± 0.89

0.67

3.58

0.024

6.88

0.000

PDK4

56

8.73 ± 0.54

7.55 ± 0.42

0.28

-2.27

0.002

-3.82

0.007

SELL

56

18.82 ± 0.88

16.10 ± 3.29

1.39

-6.60

0.101

-4.03

0.003

  

Real time PCR IN vs OUT

Affymetrix microarray

Gene

Day

IN*

OUT*

SED**

Fold Change

P -value

Fold Change

P -value

TFRC

5

9.15 ± 0.64

7.78 ± 1.20

0.56

-2.58

0.041

-5.01

0.005

CXCR4

28

9.09 ± 1.01

8.17 ± 1.18

0.63

-1.89

0.177

3.91

0.010

CCL28

56

8.61 ± 0.74

9.75 ± 0.95

0.49

2.20

0.044

2.64

0.025

CCL8

56

9.19 ± 0.80

10.44 ± 1.31

0.63

2.38

0.080

2.44

0.009

PI3

56

5.67 ± 1.26

9.16 ± 1.28

0.82

11.17

0.004

6.80

0.002

IFIT2

56

5.63 ± 2.12

7.72 ± 1.79

1.13

4.26

0.095

8.32

0.009

PDK4

56

6.68 ± 0.25

7.55 ± 0.42

0.20

1.83

0.002

1.75

0.008

SQLE

56

6.30 ± 0.92

7.40 ± 0.93

0.53

2.15

0.065

2.90

0.011

  1. Real-time PCR results at each time-point for the comparisons IR vs OUT and IN vs OUT.
  2. *PCR values are expressed as mean ΔCt ± SD, N = 6.
  3. **Standard error of difference