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Table 12 Verification of microarray results by qRT-PCR

From: Differential RelA- and RelB-dependent gene transcription in LTβR-stimulated mouse embryonic fibroblasts

Gene Symbol and GenBank Accession Number CodeLink bioarrays FC and p value (in brackets) for wt/relA-/-/relB-/- cells and corresponding subcategory qRT-PCR FC ± SD for wt/relA-/-/relB-/- cells and corresponding subcategory
Cx3cl1
NM_009142
1.77 (0.00370)/0.90 (>0.05)/0.96 (>0.05), I/1 1.66 ± 0.22/0.89 ± 0.10/1.08 ± 0.29, I/1
Pparg
NM_011146
0.65 (0.00690)/0.55 (0.01800)/1.32 (>0.05), II/2 0.50 ± 0.02/0.48 ± 0.04/0.81 ± 0.11, II/2
Ralgds *
NM_009058
2.24 (0.00750)/1.48 (>0.05)/1.58 (0.00140), III/1 2.03 ± 0.42/1.13 ± 0.10/1.17 ± 0.16, I/1 – not verified in relB-/- cells
Enpp2 *
NM_015744
2.28 (0.00150)/1.36 (>0.05)/5.10 (0.00070), III/1 1.85 ± 0.30/1.35 ± 0.27/3.29 ± 0.91, III/1
Birc3
NM_007464
2.77 (0.00090)/1.34 (>0.05)/2.94 (0.00140), III/1 2.86 ± 0.73/1.27 ± 0.11/2.99 ± 0.47, III/1
Cxcl10/IP10
NM_021274
1.91 (0.00450)/0.58 (>0.05)/2.14 (0.03000), III/1 2.58 ± 0.21/1.28 ± 0.39/2.67 ± 0.20, III/1
Irf1
NM_008390
1.96 (0.00270)/2.05 (>0.05)/2.90 (0.00075), III/1 2.67 ± 0.32/1.77 ± 0.77/2.15 ± 0.19, III/1
Cd74
NM_010545
3.11 (0.00300)/0.82 (>0.05)/3.46 (0.00070), III/1 5.01 ± 0.99/1.06 ± 0.18/4.77 ± 0.56, III/1
Fosl1
NM_010235
0.49 (0.00290)/0.86 (>0.05)/0.42 (0.00070), III/2 0.46 ± 0.09/0.90 ± 0.09/0.47 ± 0.10, III/2
Nfkb2
NM_019408
2.18 (0.0029)/1.57 (0.0016)/1.81 (0.0007), IV/1 2.04 ± 0.37/2.43 ± 0.50/2.74 ± 0.54, IV/1
Ccl2/MCP1
NM_011333
2.10 (0.00120)/2.84 (0.0011)/2.99 (0.00099), IV/1 2.29 ± 0.42/3.18 ± 0.13/6.31 ± 1.63, IV/1
Nfkbia/IκBα
NM_010907
2.00 (0.00064)/2.19 (0.00270)/3.42 (0.00140), IV/1 1.77 ± 0.16/2.44 ± 0.34/3.92 ± 0.42, IV/1
Ccl7/MCP3
NM_013654
2.22 (0.00041)/1.99 (0.04700)/4.35 (0.00140), IV/1 2.77 ± 0.13/3.15 ± 0.15/5.29 ± 1.68, IV/1
Cxcl1/KC
NM_008176
2.40 (0.00580)/1.77 (0.01600)/1.80 (0.00160), IV/1 2.40 ± 0.46/1.31 ± 0.61/3.41 ± 0.88, III/1 – not verified in relA-/- cells
Id2
NM_010496
0.42 (0.00440)/0.60 (0.04000)/0.39 (0.00075), IV/2 0.47 ± 0.11/0.75 ± 0.05/0.57 ± 0.14, IV/2
  1. qRT-PCR using RNA from 3 independent LTβR stimulation experiments confirmed changes in mRNA levels of several known as well as novel LTβR-responsive genes on the microarray. Gene names (Gene Symbol) and GenBank Accesion Numbers are shown in the first column. FC values with corresponding p values in brackets, observed in the 3 cell lines (wt; relA-/-; relB-/-) at 10 h with CodeLink bioarrays and corresponding subcategories (in bold) are displayed in the second column. FC values with corresponding standard deviations (SD), observed in the 3 cell lines (wt; relA-/-; relB-/-) at 10 h with qRT-PCR using RNA from 3 independent LTβR stimulation experiments and corresponding subcategories (in bold) are displayed in the third column. Genes that are discussed in chapter "Meta analysis of LTβR-dependent transcriptomes" are indicated by an asterisk and genes that are discussed in chapter "Verification of microarray results by qRT-PCR" are listed in bold.