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Table 2 Up-regulated genes in Smad4 null ES cells and/or day 4 embryoid bodies

From: Smad4-dependent pathways control basement membrane deposition and endodermal cell migration at early stages of mouse development

Up-regulated Embryonic Stem Cell Array Day 4 Embryoid Body Array
Gene ID Gene Description RefSeq Chr ES Array Fold Change Q-PCR data Fold Change P-value EB Array Fold Change Q-PCR data Fold Change P-value
Early ICM or ES markers
Pramel7 Preferentially expressed antigen in melanoma like 7 NM_178250 2 6.0 6.96 ± 1.09 0.002 - n.d. n.d.
Calcoco2 (Ndp52l1) Calcium binding and coiled-coil domain 2 NM_029755 11 3.0 2.66 ± 0.39 0.0112 1.45 n.d. n.d.
Zscan4 Zinc finger and SCAN domain containing 4C NM_001013765 7 2.45 2.24 ± 0.32 0.0525* 2.1 2.94 ± 0.26 0.0002
Magea8 Melanoma antigen, family A, 8 NM_020020 X 2.325 10.7 ± 0.21 < 0.0001 - n.d. n.d.
Tbx3 T-box 3 NM_011535 5 3.0 2.06 ± 0.48 0.1673* 2.6 3.78 ± 1.08 0.0544*
Pramel4 Preferentially expressed antigen in melanoma like 4 NM_001001319 4 2.0 5.26 ± 0.58 0.0212 1.5 n.d. n.d.
Germ cell markers
Tuba3a Tubulin, alpha 3A NM_009446 6 4.8 5.76 ± 0.74 0.0013 4.1 5.46 ± 0.87 0.0024
Dnmt3l DNA (cytosine-5-)-methyltransferase 3-like NM_019448 10 - n.d. n.d. 3.7 4.43 ± 0.73 0.0038
Smc1b (Smc1l2) Structural maintenance of chromosome 1b NM_080470 15 5.7 n.d. n.d. 2.8 n.d. n.d.
Dazl Deleted in azoospermia-like NM_010021 17 3.1 n.d. n.d. 1.5 n.d. n.d.
Aire Autoimmune regulator NM_009646 10 2.8 5.11 ± 0.91 0.0056 4.1 5.03 ± 1.15 0.0139
Wdr20b WD repeat domain 20b NM_027614 12 2.6 n.d. n.d. 1.45 n.d. n.d.
Endoderm markers
Dpp4 Dipeptidylpeptidase 4 NM_010074 2 2.8 n.d. n.d. 3.8 2.52 ± 0.35 0.0111
H19 H19 fetal liver mRNA NR_001592 7 2.1 1.58 ± 0.08 0.0049 2.7 3.81 ± 0.09 < 0.0001
Dab2 Disabled homolog 2 NM_023118 15 1.8 n.d. n.d. - n.d. n.d.
Dcn Decorin NM_007833 10 1.6 2.4 ± 0.27 0.0055 1.8 1.98 ± 0.56 0.1521*
Lama1 Laminin, alpha 1 NM_008480 17 - n.d. n.d. 3.9 n.d. n.d.
Hnf4a Hepatic nuclear factor 4, alpha NM_008261 2 - n.d. n.d. 1.48 n.d. n.d.
Gata6 GATA binding protein 6 NM_010258 18 4.0 8.18 ± 1.71 0.0005 - n.d. n.d.
  1. Micro-array and Q-PCR results are presented as fold change ratios relative to normalised wild-type values. The ES array results denote the average fold change of the two independent null cell lines. Genes with a 1.5 fold decrease were considered as differentially expressed. Q-PCR data is displayed as the mean ± SEM of mRNA expression levels relative to Hprt. Genes validated by Q-PCR are significantly differentially expressed (p < 0.05), except for those indicated by an asterisk. Q-PCR validation for Gata6, indicated in bold, was performed using only the FNN Smad4 null ES cell line. A subset of up-regulated genes transcripts is shown. * indicates higher than 0.05 P value for Q-PCR validation.