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.

Ling et al. Genome Biology 2009 10:R104   doi:10.1186/gb-2009-10-10-r104

Open Data