. 2022 Nov 8;115(2):224–239. doi: 10.1002/bdr2.2111

TABLE 1.

Mouse developmental regulator genes examined in the present study

Gene name	Characteristics ^a	Primer sequences (5′ ➔ 3′)
Actb	a. Cytoskeletal actin b. Ubiquitous c. Housekeeping	F: GAGAGGGAAATCGTGCGTGACATC R: CAGCTCAGTAACAGTCCGCCTAGA
Aldh1a2	a. Aldehyde dehydrogenase b. Trunk region c. Retinoic acid synthesis	F: CTTGCCTCACAACAAGTGAGCTTC R: TCACCCAGGTTAGAGACTGGCTTC
Brachyury	a. T‐box transcription factor b. Primitive streak c. Mesendoderm specification	F: CCTCGGATTCACATCGTGAGAGTT R: AGTAGGTGGGCGGGCGTTATGACT
Cdx1	a. Homeodomain transcription factor b. Primitive streak c. Axial patterning	F: TCAGGACTGGACATGAGGTAGAGG R: TGGGAAGGTGGGCATGAGCAGGTA
Cyp26a1	a. Cytochrome P450 oxidase b. Posterior end c. Retinoic acid catabolism	F: CGGAGCTGTGTAGGCAAAGAGTTT R: CCTGGAAGTGGGTAAATCTTGCAG
Dll1	a. NOTCH signaling ligand b. Posterior end c. Somite segmentation	F: TGCCCACACGTCTATCTTGGATTA R: GTCACATAGACCCGAAGTGCCTTT
Fgf8	a. FGF signaling ligand b. Primitive streak c. Mesendoderm specification	F: GTTGCACTTGCTGGTTCTCTGCCT R: AGTCCTTGCCTTTGCCGTTGCTCT
Foxc2	a. Forkhead transcription factor b. Somitic mesoderm c. Somite segmentation	F: CCCATAGGGACCCCTAATGACTTC R: GTAACAGTTGGGCAAGACGAAACC
Hes7	a. HLH transcription factor b. Posterior end c. Somite segmentation	F: CATACCCTTCTCCCACCTTTAGGC R: AGTGACGAGAAAGCGATTCAAAGG
Hoxa1	a. HOX transcription factor b. Anterior region c. Axial patterning	F: CCCTTTCCTTCCACACTGTCTTGT R: AAGACCCGTAAACTCTGCTCTGGA
Hoxb9	a. HOX transcription factor b. Posterior region c. Axial patterning	F: AAGCAGGGAGTGGTTTTATGAAGG R: GGGATAGGAATGTATGAATGGGGA
Hoxc6	a. HOX transcription factor b. Central region c. Axial patterning	F: TTCGCCACAGGAGAATGTCGTGTT R: CGAGTTAGGTAGCGGTTGAAGTGA
Lfng	a. NOTCH signaling regulator b. Posterior end c. Somite segmentation	F: AAGCAGGGAGTGGTTTTATGAAGG R: GGGATAGGAATGTATGAATGGGGA
Meox1	a. Homeodomain transcription factor b. Somitic mesoderm c. Somite differentiation	F: AAAAATCAGACTTCCCAGCGACAG R: TTCACACGTTTCCACTTCATCCTC
Mesp2	a. HLH transcription factor b. Somitic mesoderm c. Somite differentiation	F: CTGCCTTGGAAGTGCCTTTATCTG R: GATACCTAGAAGCGGGGGTGTCTT
Mixl1	a. Homeodomain transcription factor b. Primitive streak c. Mesendoderm specification	F: CGACAGACCATGTACCCAGACATC R: TGAGGCTTCAAACACCTAGCTTCA
Msgn1	a. bHLH domain transcription factor b. Posterior end c. Somite differentiation	F: CCAGAAAGGCAGCAAAGTCAAGAT R: TCTGTGAGTTCCCCGATGTACTTG
Nanog	a. Homeodomain transcription factor b. Epiblast c. Pluripotency maintenance	F: GCTTTGGAGACAGTGAGGTGCATA R: GCTACCCTCAAACTCCTGGTCCTT
Nodal	a. NODAL signaling ligand b. Epiblast c. Pluripotency maintenance	F: GTACATGTTGAGCCTCTACCGAGA R: TCTACAGACAGCTGTCCCTCCTGG
Nrarp	a. NOTCH signaling component b. Posterior end c. Somite segmentation	F: TGGGAAATAAAAGGGAGGCTGAAT R: GTGCTTGTCTCAGTGTCTGCCATT
Notch1	a. NOTCH signaling receptor b. Posterior end c. Somite segmentation	F: GTCTGCAGGCTCCAGTGTTCTGTA R: TCAGTTGGATTTGGATGATGCTGT
Sp5	a. Zinc finger transcription factor b. Primitive streak c. Wnt signaling transcriptional target	F: CAGGACAGGAAACTGGGTCGTAGT R: GGCCTAGCAAAAACTTAGGCCTTG
Pou5f1	a. POU domain transcription factor b. Epiblast c. Pluripotency maintenance	F: AGGCAGGAGCACGAGTGGAAAGCA R: GGAGGGCTTCGGGCACTTCAGAAA
Tbx6	a. T‐box transcription factor b. Posterior end c. Axial stem cell differentiation	F: GGCCTCTCTTCCACCCTTTAGTTC R: CACTAGTAACAAGGCCCCCAGGAG
Wnt3	a. WNT signaling ligand b. Primitive streak c. Initiation of gastrulation	F: CAGATGCCCGCTCAGCTATGAACA R: AGCAGCACCAGTGGAAGACGCAAT
Wnt3a	a. WNT signaling ligand b. Posterior end c. Axial stem cell differentiation	F: GCCACAAGAGCTTCCTGATTGGTA R: CCAGGCAGAAGACAGTCAGTCACC

Gene name

Characteristics ^a

Primer sequences (5′ ➔ 3′)

Actb

a. Cytoskeletal actin

b. Ubiquitous

c. Housekeeping

F: GAGAGGGAAATCGTGCGTGACATC

R: CAGCTCAGTAACAGTCCGCCTAGA

Aldh1a2

a. Aldehyde dehydrogenase

b. Trunk region

c. Retinoic acid synthesis

F: CTTGCCTCACAACAAGTGAGCTTC

R: TCACCCAGGTTAGAGACTGGCTTC

Brachyury

a. T‐box transcription factor

b. Primitive streak

c. Mesendoderm specification

F: CCTCGGATTCACATCGTGAGAGTT

R: AGTAGGTGGGCGGGCGTTATGACT

Cdx1

a. Homeodomain transcription factor

b. Primitive streak

c. Axial patterning

F: TCAGGACTGGACATGAGGTAGAGG

R: TGGGAAGGTGGGCATGAGCAGGTA

Cyp26a1

a. Cytochrome P450 oxidase

b. Posterior end

c. Retinoic acid catabolism

F: CGGAGCTGTGTAGGCAAAGAGTTT

R: CCTGGAAGTGGGTAAATCTTGCAG

Dll1

a. NOTCH signaling ligand

b. Posterior end

c. Somite segmentation

F: TGCCCACACGTCTATCTTGGATTA

R: GTCACATAGACCCGAAGTGCCTTT

Fgf8

a. FGF signaling ligand

b. Primitive streak

c. Mesendoderm specification

F: GTTGCACTTGCTGGTTCTCTGCCT

R: AGTCCTTGCCTTTGCCGTTGCTCT

Foxc2

a. Forkhead transcription factor

b. Somitic mesoderm

c. Somite segmentation

F: CCCATAGGGACCCCTAATGACTTC

R: GTAACAGTTGGGCAAGACGAAACC

Hes7

a. HLH transcription factor

b. Posterior end

c. Somite segmentation

F: CATACCCTTCTCCCACCTTTAGGC

R: AGTGACGAGAAAGCGATTCAAAGG

Hoxa1

a. HOX transcription factor

b. Anterior region

c. Axial patterning

F: CCCTTTCCTTCCACACTGTCTTGT

R: AAGACCCGTAAACTCTGCTCTGGA

Hoxb9

a. HOX transcription factor

b. Posterior region

c. Axial patterning

F: AAGCAGGGAGTGGTTTTATGAAGG

R: GGGATAGGAATGTATGAATGGGGA

Hoxc6

a. HOX transcription factor

b. Central region

c. Axial patterning

F: TTCGCCACAGGAGAATGTCGTGTT

R: CGAGTTAGGTAGCGGTTGAAGTGA

Lfng

a. NOTCH signaling regulator

b. Posterior end

c. Somite segmentation

F: AAGCAGGGAGTGGTTTTATGAAGG

R: GGGATAGGAATGTATGAATGGGGA

Meox1

a. Homeodomain transcription factor

b. Somitic mesoderm

c. Somite differentiation

F: AAAAATCAGACTTCCCAGCGACAG

R: TTCACACGTTTCCACTTCATCCTC

Mesp2

a. HLH transcription factor

b. Somitic mesoderm

c. Somite differentiation

F: CTGCCTTGGAAGTGCCTTTATCTG

R: GATACCTAGAAGCGGGGGTGTCTT

Mixl1

a. Homeodomain transcription factor

b. Primitive streak

c. Mesendoderm specification

F: CGACAGACCATGTACCCAGACATC

R: TGAGGCTTCAAACACCTAGCTTCA

Msgn1

a. bHLH domain transcription factor

b. Posterior end

c. Somite differentiation

F: CCAGAAAGGCAGCAAAGTCAAGAT

R: TCTGTGAGTTCCCCGATGTACTTG

Nanog

a. Homeodomain transcription factor

b. Epiblast

c. Pluripotency maintenance

F: GCTTTGGAGACAGTGAGGTGCATA

R: GCTACCCTCAAACTCCTGGTCCTT

Nodal

a. NODAL signaling ligand

b. Epiblast

c. Pluripotency maintenance

F: GTACATGTTGAGCCTCTACCGAGA

R: TCTACAGACAGCTGTCCCTCCTGG

Nrarp

a. NOTCH signaling component

b. Posterior end

c. Somite segmentation

F: TGGGAAATAAAAGGGAGGCTGAAT

R: GTGCTTGTCTCAGTGTCTGCCATT

Notch1

a. NOTCH signaling receptor

b. Posterior end

c. Somite segmentation

F: GTCTGCAGGCTCCAGTGTTCTGTA

R: TCAGTTGGATTTGGATGATGCTGT

Sp5

a. Zinc finger transcription factor

b. Primitive streak

c. Wnt signaling transcriptional target

F: CAGGACAGGAAACTGGGTCGTAGT

R: GGCCTAGCAAAAACTTAGGCCTTG

Pou5f1

a. POU domain transcription factor

b. Epiblast

c. Pluripotency maintenance

F: AGGCAGGAGCACGAGTGGAAAGCA

R: GGAGGGCTTCGGGCACTTCAGAAA

Tbx6

a. T‐box transcription factor

b. Posterior end

c. Axial stem cell differentiation

F: GGCCTCTCTTCCACCCTTTAGTTC

R: CACTAGTAACAAGGCCCCCAGGAG

Wnt3

a. WNT signaling ligand

b. Primitive streak

c. Initiation of gastrulation

F: CAGATGCCCGCTCAGCTATGAACA

R: AGCAGCACCAGTGGAAGACGCAAT

Wnt3a

a. WNT signaling ligand

b. Posterior end

c. Axial stem cell differentiation

F: GCCACAAGAGCTTCCTGATTGGTA

R: CCAGGCAGAAGACAGTCAGTCACC

^{^a}

Characteristics are: a—molecular function, b—major expression domains around the gastrulation stage (mouse embryonic stages from E5.5 to E8.5), and c—functional significance in early embryo development, which are based on the information available in the Mouse Genome Informatics (www.informatics.jax.org).