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Table 3 Verification of the changes in gene expression by quantitative realtime RT-PCR

From: Importance of the interferon-α system in murine large intestine indicated by microarray analysis of commensal bacteria-induced immunological changes

   Gene Name*

Gene Symbol

qt realtime RT-PCR

GeneChip

RT-PCR primer/probe ID***

  

Fold change**

p value

significant difference

GeneChip Probe Set ID

Type 1 interferon-regulatory factors

     

   interferon regulatory factor 1 (IRF1)

Irf1

1.00

-

-

Mm00515191_m1 102401_at

   interferon regulatory factor 3 (IRF3)

Irf3

1.06

0.479

-

Mm00516779_m1 99103_at

   interferon regulatory factor 5 (IRF5)

Irf5

2.38

0.112

-

Mm00496477_m1 93425_at

   interferon regulatory factor 6 (IRF6)

Irf6

1.50

0.363

-

Mm00516797_m1 92440_at

   interferon regulatory factor 7 (IRF7)

Irf7

2.44

0.031

+

Mm00516788_m1 104669_at

   interferon dependent positive acting transcription factor 3 gamma(IRF9)

Isgf3g

2.53

0.001

-

Mm00492679_m1 103634_at

   interferon consensus sequence binding protein 1(IRF8)

Irf8

1.11

0.299

-

Mm00492567_m1 98002_at

Type 1 interferon-inducible genes

     

   interferon-induced protein with tetratricopeptide repeats 1

Ifit1

5.22

0.048

+

Mm00515153_m1 100981_at

   interferon-induced protein with tetratricopeptide repeats 2

Ifit2

0.82

0.861

+

Mm00492606_m1 103639_at

   glucocorticoid-attenuated response gene 49 (GARG-49/IRG2)

Ifit3

1.99

0.195

-

Mm01704846_s1 93956_at

   guanylate nucleotide binding protein 2:mGBP-2

Gbp2

2.83

0.091

+

Mm00494575_m1 104597_at

   expressed sequence AI481100:GTPI

Iigp2

2.11

0.060

+

Mm00546343_s1 96764_at

   chemokine (C-X-C motif) ligand 10:IP-10

Cxcl10

4.69

0.058

-

Mm00445235_m1 93858_at

   interferon inducible protein 1:LRG-47, Ifi1

Irgm

6.30

0.188

+

Mm00492596_m1 97409_at

   lectin, galactose binding, soluble 9

Lgals9

1.96

0.023

+

Mm00495295_m1 103335_at

   interferon gamma induced GTPase

Igtp

2.95

0.012

+

Mm00497611_m1 160933_at

Type I interferon receptors

     

   interferon (alpha and beta) receptor 1

Ifnar1

0.29

0.424

-

Mm00439544_m1 100483_at

   interferon (alpha and beta) receptor 2

Ifnar2

1.12

0.599

+

Mm00494916_m1 101014_at

Complement-related genes

     

   complement component 1, q subcomponent, alpha polypeptide

C1qa

2.24

0.105

+

Mm00432142_m1 98562_at

   complement component 3

C3

2.74

0.059

+

Mm00437858_m1 93497_at

   serine (or cysteine) proteinase inhibitor, clade G, member 1:complement 1 inhibitor

Serping1

1.41

0.070

+

Mm00437834_m1 99081_at

MHC-related genes

     

   Histocompatibility 2, class II antigen A, alpha

H2-Aa

1.73

0.197

+

Mm01609331_m1 92866_at

   MHC class II H2-I-A-beta gene (k haplotype)

H2-AB1

1.82

0.022

+

H2-AB1-TG04 100998_at

   MHC (A.CA/J(H-2K-f) class I antigen

H2-Q1

0.88

0.496

+

Mm00657093_g1 97125_f_at

   MHC class I Q4 beta-2-microglobulin (Qb-1) gene

H2-Q4

1.65

0.008

-

H2-Q4-TG09 99378_f_at

   Q8/9d gene

LOC386462

2.22

0.017

+

H2-Q78-TG08 98438_f_at

   Histocompatibility 2, T region locus 10+17

H2-T10/22/9

1.74

0.114

+

H2-T1017-TG11 93865_s_at

   Histocompatibility 2, T region locus 23

H2-T23

1.35

0.116

+

Mm00439246_g1 98472_at

Other molecules

     

   cytotoxic T lymphocyte-associated protein 2 alpha

Ctla2a

5.17

0.002

+

Mm00484032_g1 96912_s_at

   CD52 antigen:CD80?

Cd52

2.40

0.029

+

Mm00489055_m1 104606_at

  1. * The genes giving a significant (p < 0.05) result in the real-time RT-PCR were shown in bold font.
  2. ** Fold change is defined as the ratio of the signal of GF to that of SPF.
  3. *** The primer probe sets were perchased from TaqMan Gene Expression Assays (Applied Biosystems) except for those for H2-AB1, H2-Q4, LOC386462, and H2-T10/22/9, which were synthesized by Costum TaqMan gene expression assay (Appried Byosystems) using File Builder program (Applied Byosystems). The primer-probe IDs in TaqMan Gene Expression Assays were shown in the table. The sequences of the primer-probe sets in Custom TaqMan gene expression assay are the following.
  4. H2-AB1-TG04 forward; 5'-CCTGAAGAGCCCCATCACT-3', reverse; 5'-CTTGCTCCGGGCAGACT-3', probe 5'-ACTGTGCCCTCCACTCCA-3'
  5. H2-Q4-TG09 forward;5'-CCTGGAGCTCGGGAAGGA-3', reverse; 5'-CCGTCAGATCTGTGGTGACATG-3', probe; 5'-ACAGATCCTCCAAAGGCA-3'
  6. H2-Q78-TG08 forward; 5'-AGGGCCATGAGCAGAGTTTC-3', reverse; 5'-CCCCATGTCACAGCCATACA-3', probe; 5'-AAGGGCGGCTCTCACA 3'
  7. H2-T1017-TG11 forward; 5'-ACGTGCCATGTGGACCAT-3', reverse 5'-GCAACAATCCAAATCCAAGGCTTTT-3', probe; 5'-CAGGCTCCCATCTCAG-3'
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BMC Genomics

ISSN: 1471-2164

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