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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