Table 2.
Genes examined in the present study
| Gene symbol | Descriptions* | Primer sequences (5’ ➔ 3’) |
|---|---|---|
| ACTB | Cytoplasmic actin; House keeping; Expressed broadly and constitutively (used as a loading control for normalization) | F: TACAGGAAGTCCCTTGCCATCCTA R: ACATCTCAAGTTGGGGGACAAAAA |
| ALDH1A2 | Retinal dehydrogenase; Involved in synthesis of retinoic acid; Expressed in somites | F: GTCTGTCCCTCTCTGCTTTCTCT R: TCCTCCTCCCTTTATCCCACTTTC |
| APOA1 | Apolipoprotein A; Involved in lipid metabolism; Expressed in endodermal tissues, such as liver, intestine and yolk sac | F: TGTGTACGTGGATGTGCTCAAAGA R: CTCCTGCCACTTCTTCTGGAAGTC |
| BRACHYURY | T-box transcription factor; Associated with initiation of gastrulation; Expressed in early primitive streak | F: ATCCTCATCCTCAGTTTGGAGGTG R: ACACAGGTGTCCATGAGGCTATGA |
| CDX1 | Homeodomain transcription factor; Regulates anterior-posterior axial patterning; Expressed in primitive streak | F: TCAGAGCTGGCTGCCAATC R: TGGAACCAGATCTTCACCTGC |
| EYA1 | EYA (eyes absent) transcriptional coactivator; Involved in mesoderm patterning; Expressed in mesoderm | F: CAGTCTTGACCTCTGCCTTTGTG R: AGGTTTGCTGTATTGGAGAAGCTG |
| FGF8 | Ligand for FGF signaling; Regulates mesoderm patterning and behavior; Expressed in primitive streak | F: AGCAGAGTTCGAGTCCGAGGAG R: CAGCGCTGTGTAGTTGTTCTCCA |
| FOXA1 | Forkhead transcription factor; Regulates endoderm differentiation; Expressed in endoderm lineages | F: CAAACCAAACCGTCAACAGCATAA R: GGGCAAGGAAGGAGGAGAATTT |
| FOXC2 | Forkhead transcription factor; Involved in mesoderm patterning; Expressed in paraxial mesoderm | F: GTCTGTGAAGAGCGCAGGTAACTT R: GGGCTCGCTATGGGATTTGGTC |
| GAPDH | Glyceraldehyde 3-phosphate dehydrogenase; House keeping; Expressed broadly and constitutively | F: TAGAAAAACCTGCCAAATATGATG R: GTCTCTCTCTTCCTCTTGTGCTCT |
| GATA6 | GATA transcription factor; Involved in endoderm specification; Expressed in endoderm lineages | F: AACTACCACCTTATGGCGCAGAAA R: CCCATCTTGACCCGAATACTTGAG |
| HES7 | HLH transcription factor; Involved in somite segmentation; Expressed in presomitic mesoderm | F: ACCCGGGATCGAGCTGAGAATAG R: ACTCGCGGAAACCGGACAAGTAG |
| HOXB1 | HOX transcription factor; Involved in anterior-posterior axial patterning; Expressed in a gradient along body axis | F: CGGGCCTTCTCAGTACTACCCTCT R: TCTGGAACCAAATCTTGACCTGTG |
| HOXB3 | HOX transcription factor; Involved in anterior-posterior axial patterning; Expressed in a gradient along body axis | F: GGGATGGTGAGAGATCCTGAAAGA R: CTCGTGTCACCAACTGCTTTCTGT |
| HOXB5 | HOX transcription factor; Involved in anterior-posterior axial patterning; Expressed in a gradient along body axis | F: GCCAATTTCACCGAAATAGACGAG R: CCAAACGAAATATCGTAACACAAGG |
| HOXB7 | HOX transcription factor; Involved in anterior-posterior axial patterning; Expressed in a gradient along body axis | F: GGAGGGAGAAAGGAGAAATTTTGG R: GGTTAGTCCAGACCCACAGTCCAC |
| HOXB9 | HOX transcription factor; Involved in anterior-posterior axial patterning; Expressed in a gradient along body axis | F: GAGCCTTGACAATGTTGTCCTCCT R: ACGGAAGGTGGAGGGATTTTTCTA |
| IHH | Ligand for Hedgehog signaling; Involved in body patterning; Expressed in the primitive endoderm | F: CCCGTCGTGGTGTAGTCATAGAG R: CCCAGGGAATTTAGCAGCATCAA |
| MEOX1 | Homeodomain transcription factor; Regulates somite segmentation; Expressed in somites | F: GGGCTGAACAACTAGGAGCTGAAA R: GAGGGATTTTCTTGTCCCCTTTTG |
| MESP2 | HLH transcription factor; Involved in somite segmentation; Expressed in unsegmented paraxial mesoderm | F: GTAGCTTGGGTGCCTCCTTATTTG R: CCCTTCTTAGAGCAGCTCAGACT |
| MPP1 | Palmitoylated membrane protein; Expressed in endoderm tissues, such as liver and intestine | F: GAATTCCACCCGCCTTGCTTTA R: TTGCTGTGCATCACCCTTGATTAG |
| MSGN1 | HLH transcription factor; Regulates somite patterning; Expressed in unsegmented paraxial mesoderm | F: GCCTGGTAGAGGTGGACTACAATA R: TGAGTGTCTGGATCTTGGTGAGAG |
| NANOG | Homeodomain transcription factor; Regulates pluripotency maintenance; Expressed in epiblast | F: TGAAGCATCCGACTGTAAAGAATC R: CATTGCTATTCTTCGGCCAGTTGT |
| NEUROG2 | HLH transcription factor; Regulates neural differentiation; Expressed in neural tube | F: TCCTCGGTTGTTTCTTGCATTTCT R: AGATCACAGGAACCAGTTGCATTC |
| NODAL | Ligand for Nodal signaling; Inducer of endoderm specification; Expressed in primitive endoderm and primitive streak | F: GACATCATCCGCAGCCTACAGG R: GACCTGGGACAAAGTGACAGTG |
| OLIG3 | HLH transcription factor; Involved in neural patterning; Expressed in neural tube | F: AGAGATCTCAGACTCCACTTGACC R: CACAGAGTCAGAGAAAGCCAACTC |
| PAX3 | Paired-box transcription factor; Involved in somite and neural patterning; Expressed in somites and neural tube | F: GTACACCAAAGCACGATTCCTT R: GCTATAGGTGGGTGGACAGTAG |
| PAX6 | Paired-box transcription factor; Involved in neural specification and patterning; Expressed in neuroectoderm | F: TGTCTTCCCTAGAAATCCTCAGAATGA R: ACAAAATGATTGGACCGTGAACAG |
| POU5F1 | POU-domain transcription factor; Regulates pluripotency maintenance; Expressed in epiblast | F: TGGTGCCGTGAAGCTGGAGAAGGA R: CTGCTTGATCGCTTGCCCTTCTGG |
| SOX17 | SRY-box transcription factor; Involved in endoderm specification; Expressed in endoderm lineages | F: CAAAGAAATGTTGTCCTGGGTGTG R: GTTCACCCTTTTCGAGGATGAGAA |
| SOX2 | SRY-box transcription factor; Regulates pluripotency maintenance; Expressed in epiblast and neural tube | F: CCCCCGGCGGCAATAGCA R: TCGGCGCCGGGGAGATACAT |
| TBX6 | T-box transcription factor; Involved in paraxial mesoderm specification; Expressed in caudal end | F: ATCTCCGTGACAGCCTACCAGAAC R: AGTACATGGGTTTGGAGCCCACAT |
| TCF15 | HLH transcription factor; Regulates patterning of paraxial mesoderm; Expressed in somites | F: CCATCTGCACCTTCTGCCTCAG R: CCCGGTCCCTACACAAAGAAGG |
| UNCX | Homeodomain transcription factor; Involved in segmentation of paraxial mesoderm; Expressed in somites | F: CTCAGGCTCCGACTCACGCAAC R: CTCTCTTGGGAGGAGGAGGGTCTC |
| WNT3A | Ligand for Wnt signaling; Regulates paraxial mesoderm specification; Expressed in late primitive streak | F: AGTGACACGCTCATGTGCAGAA R: GAAGGAGCCCGTCTCAGGGTTG |
| WNT5A | Ligand for Wnt signaling; Regulates axial elongation; Expressed at caudal end | F: CTACCGCTTTGCCAAGGAGTTC R: CGTACTTCTCCTTCAGGGCATCA |
*
Molecular features, functional roles and expression patterns during early embryogenesis are largely based on studies in the mouse(Mouse Genome Informatics: www.informatics.jax.org).