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Table 3 RT-qPCR validation of SAGE profile for E versus adult comparison

From: Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

    Fold change
SAGE tag RefSeq accession Gene ID Ad/E15.5 (SAGE) Ad/E17.5 (SAGE) Ad/E15.5 (RT-qPCR) Ad/E17.5 (RT-qPCR)
gcttccccacccccctt NM_177407 calcium/calmodulin-dependent protein kinase II alpha, Camk2a As As 111.59 54.74
ggatatgtggtgtgtac NM_007913 early growth response 1, Egr1 As As 108.47 38.93
aaattattgggaaatcc NM_011123 proteolipid protein (myelin) 1, Plp1 28.77 As 103.15 89.13
gtatttgcaaaaaaaaa NM_025451 calcium/calmodulin-dependent protein kinase II inhibitor 1, Camk2n1 69.59 59.76 40.08 21.46
gcttcatctccagggag NM_009964 crystallin, alpha B, Cryab As 11.59 30.47 20.58
ttaccatactgggttgg NM_022029 neurogranin, Nrgn 24.67 8.47 43.67 17.00
cctcatttcccctgttc BQ176089 EST from adult C57BL/6 subfornical organ and postrema tissues As As 23.01 8.91
acccggctagtagtgaa NM_011129 septin 4, Sept4 18.97 16.29 22.38 12.96
ctcattataatcaagaa CD802535 EST from 27-32 days C57BL/6 hippocampus tissue As 9.05 22.03 13.25
aataaagccaatctgac NM_033610 synuclein, beta, Sncb 20.89 7.66 18.20 15.83
gcttttgttaccatctc NM_030689 neuronal pentraxin receptor, Nptxr 17.88 12.24 15.02 10.93
tccctcccttagtatcc NM_144828 protein phosphatase 1, regulatory (inhibitor) subunit 1B, Ppp1r1b As As 10.47 6.88
gccccttcttcattggc NM_010358 glutathione S-transferase, mu 1, Gstm1 As As 9.87 5.58
tgactagcgtgacctgt NM_007694 chromogranin B, Chgb 6.13 6.30 9.43 7.22
atttcttttctggatgg NM_010585 inositol 1,4,5-triphosphate receptor 1, Itpr1 14.34 6.16 9.29 6.12
actttgagattgtacct NM_009062 regulator of G-protein signaling 4, Rgs4 12.23 21.01 8.84 5.32
aataattagccttaggt AK139402 Mus musculus 10 days neonate cortex cDNA As As 8.28 7.55
ctagacagaggcattat NM_019634 tetraspanin 7, Tspan7 13.08 5.61 7.99 5.38
tgtatacacacacgggt NM_007547 signal-regulatory protein alpha, Sirpa As As 7.18 4.63
tgacaagacactgtggc AU258168 EST from mouse brain As As 6.49 4.58
cttacctcaggtttcct NM_008913 protein phosphatase 3, catalytic subunit, alpha isoform, Ppp3ca As 5.43 5.48 3.45
atagctttctacacact NM_007471 amyloid beta (A4) precursor protein, App 3.98 2.74 4.56 3.49
tttcagcagtgttggct NM_013556 hypoxanthine guanine phosphoribosyl transferase 1, Hprt1 6.90 8.87 3.45 2.85
aggtatgtacaaagttt NM_016886 glutamate receptor, ionotropic, AMPA3 (alpha 3), Gria3 4.97 8.51 3.40 1.81*
tccaacttgtaactata NM_009790 calmodulin 1, Calm1 4.23 3.17 3.24 2.27
cctcagcctggggtaga NM_009983 cathepsin D, Ctsd 3.46 2.04 3.22 3.84
gcttcgtccacacagcg NM_010777 myelin basic protein, Mbp 202.46 173.85 3.19 2.05
tattaaatgtgcttttt NM_080555 phosphatidic acid phosphatase type 2B, Ppap2b 5.71 2.44 3.02 2.76
cttatcctcacctcagc NC_005089 NADH dehydrogenase 6, mitochondrial, mt-ND6 As As 2.65 2.13
caaacctccaaaaacca AK140219 Mus musculus adult male corpora quadrigemina cDNA 29.22 18.62 2.63 2.03
agtggctaattaggtgt NM_009900 chloride channel 2, Clcn2 14.55 4.16 2.23 2.18
accaatgaacaaaaaaa AK154943 Mus musculus NOD-derived CD11c +ve dendritic cells cDNA 109.40 51.13 1.76* 1.35 (NS)
ccagtacctgaaaaaaa NM_008453 Kruppel-like factor 3 (basic), Klf3 As -52.97 -1.47†‡ -1.27 (NS)
aagaaaacatttaaata NM_012010 eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked, Eif2s3x -7.70 -10.38 -1.72* -1.74*
caccctgtgggagctca NM_172656 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2 (human), Als2cr2 -11.03 -12.88 -1.75* -2.48
cctccatcctttatact NM_009536 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide, Ywhae -3.19 -2.52 -1.82* -2.66
tgtgcttccctgtctta NM_008683 neural precursor cell expressed, developmentally down-regulated gene 8, Nedd8 -4.73 -8.41 -1.83 -1.86
ctcctgaaggcatagtt NM_009454 ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast), Ube2e3 -4.14 -5.52 -2.51 -3.22
gtgaaactaaaaaaaaa NM_009094 ribosomal protein S4, X-linked, Rps4x -10.46 -19.19 -2.76 -3.35
aatgtttctgctttaca NM_011045 proliferating cell nuclear antigen, Pcna -14.21 -8.30 -3.09 -2.62
cgtggatccctctgtca NM_009876 cyclin-dependent kinase inhibitor 1C (P57), Cdkn1c -13.68 -7.16 -3.39* -3.30*
cctttgtgacagtggcc NM_025635 ZW10 interactor, Zwint 7.29 8.84 -3.47‡ -4.80‡
gaagccagtgggccatc NM_001033273 RIKEN cDNA 5031439G07 gene, 5031439G07Rik -9.10 -10.00 -4.13 -3.65
gctgtgggtcgctgtgg NM_010561 interleukin enhancer binding factor 3, Ilf3 As As -4.15‡ -2.97‡
acccctgaccccttgtt NM_016707 B-cell CLL/lymphoma 11A (zinc finger protein), Bcl11a -7.88 -5.52 -4.42 -4.78
cggtgtcccccacctcc NM_012015 H2A histone family, member Y, H2afy -21.48 -27.88 -4.62 -3.70
cagttgcaataaaaata NM_010894 neurogenic differentiation 1, Neurod1 -7.54 -4.96 -5.62 -5.10
aagtttgcaagtctcca NM_008538 myristoylated alanine rich protein kinase C substrate, Marcks -24.87 -11.76 -5.72 -5.56
ttgctggcttttataaa NM_053104 RNA binding motif protein 9, Rbm9 -6.10 -7.82 -6.50 -5.97
ggttttgtttgtttgac NM_019653 WD repeat and SOCS box-containing 1, Wsb1 -7.88 -11.96 -6.54 -7.00
tatattgattgtggcaa NM_007569 B-cell translocation gene 1, anti-proliferative, Btg1 -15.28 -16.48 -6.93 -5.58
taagaaacct NM_019413 roundabout homolog 1 (Drosophila), Robo1 -28.64 -16.73 -8.23 -11.35
gctttgactgttctctt AA122503 EST from M2 cells of skin melanoma -17.17 -18.68 -9.88 -10.15
tggagcgttggctgtat NM_009870 cyclin-dependent kinase 4, Cdk4 -114.55 -80.88 -14.77 -10.00
ctttccctgccaatgta NM_013834 secreted frizzled-related protein 1, Sfrp1 Es Es -16.48 -16.37
tgcagctttctgttcaa NM_007971 enhancer of zeste homolog 2 (Drosophila), Ezh2 -10.63 -5.52 -21.36 -17.59
cacgacaccccccaccc NM_009559 zinc finger protein 57, Zfp57 -30.72 -42.33 -29.13 -44.46
tgtgtgaggtgttgtga NM_010025 doublecortin, Dcx -44.41 -58.81 -73.76 -91.10
cagagtgtagtgtgttg NM_009234 SRY-box containing gene 11, Sox11 Es Es -140.05 -120.35
  1. All RT-qPCR data are statistically significant at P < 0.001 unless specified: * P < 0.01; †P < 0.05. ‡A disagreement between RT-qPCR and SAGE data. As, adult-specific expression; Es, embryonic-specific expression; NS, no statistically significant difference between two developmental stages. Fold change values of <1.0 are presented in a negative fold change format.
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Genome Biology

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