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Table 2 Differential expression data based on array experiments and Q-PCR of ectoderm marker genes

From: A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks

Ectoderm markers Expression Regulation P value Q-PCR ratio ± error
Bmp2/4
SpSMBLIT_68K21
Oral Li 1.32
Zn 1.54
3.13 × e-01
7.33 × e-01
1.27 ± 0.29
0.97 ± 0.25
Chordin
537REA_13L23
Oral Li nd
Zn 0.40
nd
4.55 × e-05
1.19 ± 0,19
0.41 ± 0,12
Goosecoid
RUDIREA_9C8
Oral Li 1.05
Zn 0.27
8.43 × e-01
4.13 × e-03
0.75 ± 0.08a
0.16 ± 0.06
Lefty
536REAsu4_7H9
Oral Li 1.80
Zn nd
1.91 × e-07
nd
0.98 ± 0.22a
2.17 ± 0,14
Nodal
536REA_98I13
Oral Li na
Zn na
na
na
1.34 ± 0,11
4.12 ± 0,23
IrxA
SpSMBLAS_51E6
Aboral Li 0.38
Zn
2.51 × e-09 0.08 ± 0.05
1.60 ± 0.02
Nkx2.2
536REAsu4_10G11
Aboral Li 0.37
Zn nd
7.69 × e-08
nd
0.15 ± 0.13
5.87 ± 0.15
Spec2A Aboral Li nd
Zn nd
nd
nd
na
10.64 ± 1.67
Tbx2
RUDIREA_26D12
Aboral Li 0.20
Zn
3.50 × e-12 0.12 ± 0.01
1.42 ± 0.24
Dp-Hbn
SpSMBLAS_141N1
Apical Li 0.14
Zn nd
1.41 × e-07
nd
0.05 ± 0.02
1.03 ± 0.21
FoxJ
RUDIREA_13I13
Apical Li 1.40
Zn 2.29
2.86 × e-02
3.26 × e-07
0.93 ± 0.20a
1.84 ± 0.04
FoxQ
537REA_3F18
Apical Li 0.24
Zn 4.51
3.55 × e-14
5.01 × e-07
0.15 ± 0.03
4.66 ± 0.78
Glass
536REAsu2_5I1
Apical Li 0.52
Zn na
2.99 × e-01
na
ne
0.03± 0.01
ZFhpf4
537REA_15C23
Apical Li 0.24
Zn na
7.78 × e-07
na
1.20 ± 0.00
2.05 ± 0.15
Hypothetical
RUDIREA_15C22
Apical + SMC late Li 0.59
Zn 4.27
4.79 × e-01
3.24 × e-02
0.20 ± 0.06
1.11 ± 0.10
Mox
SpSMBLAS_131A20
Apical, serotonergic Li 0.49
Zn nd
8.23 × e-02
nd
1.76 ± 0.22a
1.39 ± 0.21
Radical spoke protein
RUDIREA_39F2
Apical Li 1.56
Zn na
5.75 × e-04
na
1.14 ± 0.10
2.11 ± 0.45
sFRP1/5
536REAsu4_11O4
Apical Li 0.42
Zn 1.99
7.10 × e-04
3.67 × e-04
0.11 ± 0.04
2.14 ± 0.08
Hairy1
537REA_10P14
Cilliary band +?E Li 0.77
Zn
5.78 × e-06 0.62 ± 0.04
1.54 ± 0.25
onecut
538REA_9E3
Cilliary band Li 0.40
Zn 0.74
3.20 × e-04
5.88 × e-03
0.68 ± 0.06
1.84 ± 0.24a
Pax2
RUDIREA_22J20
Cilliary band Li 1.14
Zn na
7.71 × e-01
na
3.72 ± 0.50
0.11 ± 0.02
AEX3
RUDIREA_5J10
Entire ectoderm, off vegetal Li 0.64
Zn 5.34
1.37 × e-08
3.83 × e-12
0.78 ± 0.26
9.11 ± 0.90
Hatching enzyme
538REA_2G05
Entire ectoderm Li 3,39
Zn 4.35
4.42 × e-07
1.25 × e-03
7.55 ± 0.55
11.42 ± 0.87
Otx
537REA_12D12
Entire ectoderm Li 0.65
Zn na
1.01 × e-04
na
0.96 ± 0.09
2.43 ± 0.14
Soxb1
RUDIREA_25A17
Entire ectoderm Li 1.28
Zn nd
9.93 × e-02
nd
0.87 ± 0.05a
1.43 ± 0.27
Soxb2
536REAsu4_4A13
Entire ectoderm Li 1.44
Zn
6.71 × e-05 0.79 ± 0.12a
1.12 ± 0.27
SpAN
RUDIREA_29D20
Entire ectoderm Li 2.19
Zn nd
7.72 × e-07
nd
1.88 ± 0.13
1.73 ± 0.14
  1. The first column gives the gene name and the clone ID, both of which can be used to query the described database [22] for additional data. In the second column the localization of expression in the embryo is given, where E is endoderm and SMC is secondary mesenchyme cell. The third column (Regulation) gives the differential expression ratios (expression in treatment/expression control) based on the array experiment for lithium (Li) and zinc (Zn) treated embryos (values above 1 indicate upregulation and values below 1 indicate downregulation). The column 'P value' indicates the statistical probability that the regulation could happen by chance (see Materials and methods for detail). The column Q-PCR (quantitative real-time polymerase chain reaction) gives the differential expression ratios (expression in treatment/expression control) and the error, as determined by Q-PCR. (Values expressed in copies of mRNA molecules/embryo are provided via the expressed sequence tag database [75]; see Materials and methods for details on Q-PCR). aDifferential expression based on array and Q-PCR data do not correlate. na, not analyzed; nd, no statistically relevant differential expression; ne, not expressed; ?, expression pattern unknown.