Table 3 |
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|
RT-qPCR validation of SAGE profile for E versus adult comparison |
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|
Fold change |
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|
|
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|
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 |
calcium/calmodulin-dependent protein kinase II alpha, Camk2a |
As |
As |
111.59 |
54.74 |
|
|
ggatatgtggtgtgtac |
early growth response 1, Egr1 |
As |
As |
108.47 |
38.93 |
|
|
aaattattgggaaatcc |
proteolipid protein (myelin) 1, Plp1 |
28.77 |
As |
103.15 |
89.13 |
|
|
gtatttgcaaaaaaaaa |
calcium/calmodulin-dependent protein kinase II inhibitor 1, Camk2n1 |
69.59 |
59.76 |
40.08 |
21.46 |
|
|
gcttcatctccagggag |
crystallin, alpha B, Cryab |
As |
11.59 |
30.47 |
20.58 |
|
|
ttaccatactgggttgg |
neurogranin, Nrgn |
24.67 |
8.47 |
43.67 |
17.00 |
|
|
cctcatttcccctgttc |
EST from adult C57BL/6 subfornical organ and postrema tissues |
As |
As |
23.01 |
8.91 |
|
|
acccggctagtagtgaa |
septin 4, Sept4 |
18.97 |
16.29 |
22.38 |
12.96 |
|
|
ctcattataatcaagaa |
EST from 27-32 days C57BL/6 hippocampus tissue |
As |
9.05 |
22.03 |
13.25 |
|
|
aataaagccaatctgac |
synuclein, beta, Sncb |
20.89 |
7.66 |
18.20 |
15.83 |
|
|
gcttttgttaccatctc |
neuronal pentraxin receptor, Nptxr |
17.88 |
12.24 |
15.02 |
10.93 |
|
|
tccctcccttagtatcc |
protein phosphatase 1, regulatory (inhibitor) subunit 1B, Ppp1r1b |
As |
As |
10.47 |
6.88 |
|
|
gccccttcttcattggc |
glutathione S-transferase, mu 1, Gstm1 |
As |
As |
9.87 |
5.58 |
|
|
tgactagcgtgacctgt |
chromogranin B, Chgb |
6.13 |
6.30 |
9.43 |
7.22 |
|
|
atttcttttctggatgg |
inositol 1,4,5-triphosphate receptor 1, Itpr1 |
14.34 |
6.16 |
9.29 |
6.12 |
|
|
actttgagattgtacct |
regulator of G-protein signaling 4, Rgs4 |
12.23 |
21.01 |
8.84 |
5.32 |
|
|
aataattagccttaggt |
Mus musculus 10 days neonate cortex cDNA |
As |
As |
8.28 |
7.55 |
|
|
ctagacagaggcattat |
tetraspanin 7, Tspan7 |
13.08 |
5.61 |
7.99 |
5.38 |
|
|
tgtatacacacacgggt |
signal-regulatory protein alpha, Sirpa |
As |
As |
7.18 |
4.63 |
|
|
tgacaagacactgtggc |
EST from mouse brain |
As |
As |
6.49 |
4.58 |
|
|
cttacctcaggtttcct |
protein phosphatase 3, catalytic subunit, alpha isoform, Ppp3ca |
As |
5.43 |
5.48 |
3.45 |
|
|
atagctttctacacact |
amyloid beta (A4) precursor protein, App |
3.98 |
2.74 |
4.56 |
3.49 |
|
|
tttcagcagtgttggct |
hypoxanthine guanine phosphoribosyl transferase 1, Hprt1 |
6.90 |
8.87 |
3.45 |
2.85 |
|
|
aggtatgtacaaagttt |
glutamate receptor, ionotropic, AMPA3 (alpha 3), Gria3 |
4.97 |
8.51 |
3.40 |
1.81* |
|
|
tccaacttgtaactata |
calmodulin 1, Calm1 |
4.23 |
3.17 |
3.24 |
2.27 |
|
|
cctcagcctggggtaga |
cathepsin D, Ctsd |
3.46 |
2.04 |
3.22 |
3.84 |
|
|
gcttcgtccacacagcg |
myelin basic protein, Mbp |
202.46 |
173.85 |
3.19 |
2.05 |
|
|
tattaaatgtgcttttt |
phosphatidic acid phosphatase type 2B, Ppap2b |
5.71 |
2.44 |
3.02 |
2.76 |
|
|
cttatcctcacctcagc |
NADH dehydrogenase 6, mitochondrial, mt-ND6 |
As |
As |
2.65 |
2.13 |
|
|
caaacctccaaaaacca |
Mus musculus adult male corpora quadrigemina cDNA |
29.22 |
18.62 |
2.63 |
2.03 |
|
|
agtggctaattaggtgt |
chloride channel 2, Clcn2 |
14.55 |
4.16 |
2.23 |
2.18 |
|
|
accaatgaacaaaaaaa |
Mus musculus NOD-derived CD11c +ve dendritic cells cDNA |
109.40 |
51.13 |
1.76* |
1.35 (NS) |
|
|
ccagtacctgaaaaaaa |
Kruppel-like factor 3 (basic), Klf3 |
As |
-52.97 |
-1.47†‡ |
-1.27 (NS) |
|
|
aagaaaacatttaaata |
eukaryotic translation initiation factor 2, subunit 3, structural gene X-linked, Eif2s3x |
-7.70 |
-10.38 |
-1.72* |
-1.74* |
|
|
caccctgtgggagctca |
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2 (human), Als2cr2 |
-11.03 |
-12.88 |
-1.75* |
-2.48 |
|
|
cctccatcctttatact |
tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide, Ywhae |
-3.19 |
-2.52 |
-1.82* |
-2.66 |
|
|
tgtgcttccctgtctta |
neural precursor cell expressed, developmentally down-regulated gene 8, Nedd8 |
-4.73 |
-8.41 |
-1.83 |
-1.86 |
|
|
ctcctgaaggcatagtt |
ubiquitin-conjugating enzyme E2E 3, UBC4/5 homolog (yeast), Ube2e3 |
-4.14 |
-5.52 |
-2.51 |
-3.22 |
|
|
gtgaaactaaaaaaaaa |
ribosomal protein S4, X-linked, Rps4x |
-10.46 |
-19.19 |
-2.76 |
-3.35 |
|
|
aatgtttctgctttaca |
proliferating cell nuclear antigen, Pcna |
-14.21 |
-8.30 |
-3.09 |
-2.62 |
|
|
cgtggatccctctgtca |
cyclin-dependent kinase inhibitor 1C (P57), Cdkn1c |
-13.68 |
-7.16 |
-3.39* |
-3.30* |
|
|
cctttgtgacagtggcc |
ZW10 interactor, Zwint |
7.29 |
8.84 |
-3.47‡ |
-4.80‡ |
|
|
gaagccagtgggccatc |
RIKEN cDNA 5031439G07 gene, 5031439G07Rik |
-9.10 |
-10.00 |
-4.13 |
-3.65 |
|
|
gctgtgggtcgctgtgg |
interleukin enhancer binding factor 3, Ilf3 |
As |
As |
-4.15‡ |
-2.97‡ |
|
|
acccctgaccccttgtt |
B-cell CLL/lymphoma 11A (zinc finger protein), Bcl11a |
-7.88 |
-5.52 |
-4.42 |
-4.78 |
|
|
cggtgtcccccacctcc |
H2A histone family, member Y, H2afy |
-21.48 |
-27.88 |
-4.62 |
-3.70 |
|
|
cagttgcaataaaaata |
neurogenic differentiation 1, Neurod1 |
-7.54 |
-4.96 |
-5.62 |
-5.10 |
|
|
aagtttgcaagtctcca |
myristoylated alanine rich protein kinase C substrate, Marcks |
-24.87 |
-11.76 |
-5.72 |
-5.56 |
|
|
ttgctggcttttataaa |
RNA binding motif protein 9, Rbm9 |
-6.10 |
-7.82 |
-6.50 |
-5.97 |
|
|
ggttttgtttgtttgac |
WD repeat and SOCS box-containing 1, Wsb1 |
-7.88 |
-11.96 |
-6.54 |
-7.00 |
|
|
tatattgattgtggcaa |
B-cell translocation gene 1, anti-proliferative, Btg1 |
-15.28 |
-16.48 |
-6.93 |
-5.58 |
|
|
taagaaacct |
roundabout homolog 1 (Drosophila), Robo1 |
-28.64 |
-16.73 |
-8.23 |
-11.35 |
|
|
gctttgactgttctctt |
EST from M2 cells of skin melanoma |
-17.17 |
-18.68 |
-9.88 |
-10.15 |
|
|
tggagcgttggctgtat |
cyclin-dependent kinase 4, Cdk4 |
-114.55 |
-80.88 |
-14.77 |
-10.00 |
|
|
ctttccctgccaatgta |
secreted frizzled-related protein 1, Sfrp1 |
Es |
Es |
-16.48 |
-16.37 |
|
|
tgcagctttctgttcaa |
enhancer of zeste homolog 2 (Drosophila), Ezh2 |
-10.63 |
-5.52 |
-21.36 |
-17.59 |
|
|
cacgacaccccccaccc |
zinc finger protein 57, Zfp57 |
-30.72 |
-42.33 |
-29.13 |
-44.46 |
|
|
tgtgtgaggtgttgtga |
doublecortin, Dcx |
-44.41 |
-58.81 |
-73.76 |
-91.10 |
|
|
cagagtgtagtgtgttg |
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. |
||||||
|
Ling et al. Genome Biology 2009 10:R104 doi:10.1186/gb-2009-10-10-r104 |
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