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