Table 1.
Primers Used for RT-PCR and PCR
| Description and Genes | Symbol | Gene ID | Primer Sequence (5′ to 3′) | ||
|---|---|---|---|---|---|
| Transgene detection | |||||
| POU class 5 homeobox 1 | OCT3/4Tg | 5460 | S | CCCCAGGGCCCCATTTTGGTACC | |
| A | TTATCGTCGACCACTGTGCTGCTG | ||||
| SRY (sex-determining region Y)-box 2 | SOX2Tg | 6657 | S | GGCACCCCTGGCATGGCTCTTGGCTC | |
| A | TTATCGTCGACCACTGTGCTGCTG | ||||
| v-Myc myelocytomatosis viral oncogene homolog | MYCTg | 4609 | S | CAACAACCGAAAATGCACCAGCCCCAG | |
| A | TTATCGTCGACCACTGTGCTGCTG | ||||
| Krüppel-like factor 4 | KLF4Tg | 9314 | S | ACGATCGTGGCCCCGGAAAAGGACC | |
| A | TTATCGTCGACCACTGTGCTGCTG | ||||
| Expression of hES markers | |||||
| POU class 5 homeobox 1 | OCT3/4 | 5460 | S | GACAGGGGGAGGGGAGGAGCTAGG | |
| A | CTTCCCTCCAACCAGTTGCCCCAAAC | ||||
| SRY (sex-determining region Y)-box 2 | SOX2 | 6657 | S | GGGAAATGGGAGGGGTGCAAAAGAGG | |
| A | TTGCGTGAGTGTGGATGGGATTGGTG | ||||
| v-Myc myelocytomatosis viral oncogene homolog | MYC | 4609 | S | GCGTCCTGGGAAGGGAGATCCGGAGC | |
| A | TTGAGGGGCATCGTCGCGGGAGGCTG | ||||
| Krüppel-like factor 4 | KLF4 | 9314 | S | ACGATCGTGGCCCCGGAAAAGGACC | |
| A | TGATTGTAGTGCTTTCTGGCTGGGCTCC | ||||
| Nanog homeobox | NANOG | 79923 | S | GCAGAAGGCCTCAGCACCTA | |
| A | GGTTCCCAGTCGGGTTCAC | ||||
| Telomerase reverse transcriptase | TERT | 7015 | S | CTCCATCCTGAAAGCCAAGAA | |
| A | CGAGTCAGCTTGAGCAGGAA | ||||
| X (inactive)-specific transcript(nonprotein coding) | XIST | 7503 | S | TGGCAGGGAGTGCCAGCTCCA | |
| A | GACCAAGGTGCATGGCTGCGGT | ||||
| Expression of endoderm markers | |||||
| Forkhead box A2 | FOXA2 | 3170 | S | TGCTGGTCGTTTGTTGTGG | |
| A | CATGTTGCTCACGGAGGAGTAG | ||||
| GATA binding protein 4 | GATA4 | 2626 | S | CTCTTCAGGCAGTGAGAGCC | |
| A | GGTCCGTGCAGGAATTTGAGG | ||||
| SRY (sex-determining region Y)-box 17 | SOX17 | 64321 | S | CCCATAGTTGGATTGTCAAAACC | |
| A | CACACCCAGGACAACATTTCTTT | ||||
| α-Fetoprotein | AFP | 174 | S | TTGAGAAACCCACTGGAGATGA | |
| A | GTTATGTCTTCCCTCTTCACTTTGG | ||||
| Albumin | ALB | 213 | S | GTTGCATGAGAAAACGCCAGTA | |
| A | AGCATGGTCGCCTGTTCAC | ||||
| Expression of mesoderm markers | |||||
| T, brachyury homolog (mouse) | Brachyury | 6862 | S | TGGAATGCCTGCCCATC | |
| A | CCGTTGCTCACAGACCACA | ||||
| NK2 transcription factor related, locus 5 | NKX2-5 | 1482 | S | CCCCTGGATTTTGCATTCAC | |
| A | CGTGCGCAAGAACAAACG | ||||
| Msh homeobox 1 | MSX1 | 4487 | S | CAGAAGATGCGCTCGTCAAA | |
| A | CGGCTTACGGTTCGTCTTG | ||||
| Collagen, type II, α1 | COL2A1 | 1280 | S | GGAAGAGTGGAGACTACTGGATTGAC | |
| A | TCCATGTTGCAGAAAACCTTCA | ||||
| Expression of neural markers | |||||
| Neurogenin 2 | NEUROG2 | 63973 | S | ATGCCTATTGTCCTGTCCTTCTCT | |
| A | TGACTTCTAACCTGCCCCTCTAAC | ||||
| SRY (sex-determining region Y)-box 1 | SOX1 | 6656 | S | AGCAGTTGTTTCTGGAAGAGTCTGT | |
| A | AGGCCCTTATCCCGGACTAA | ||||
| Paired box 6 | PAX6 | 5080 | S | ACCTGGCTAGCGAAAAGCAA | |
| A | CCCGTTCAACATCCTTAGTTTATCA | ||||
| Expression of astrocyte marker | |||||
| Glial fibrillary acidic protein | GFAP | 2670 | S | ACATCGAGATCGCCACCTAC | |
| A | ACATCACATCCTTGTGCTCC | ||||
| Expression of Epidermis marker | |||||
| Keratin 17 | KRT17 | 3872 | S | AGGAGATTGCCACCTACCG | |
| A | CTTGCCATCCTGGACCTCTT | ||||
| Expression of other genes | |||||
| v-Myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived | MYCL1 | 4610 | S | CGAGAGCCCAAGCGACTCGGAGAA | |
| A | CAGGGGGTCTGCTCGCACCG | ||||
| GLIS family zinc finger 1 | GLIS1 | 148979 | S | TCTGCCCAGCCCACAAGGTTACCA | |
| A | GGCAGCGCTGTGGGGCATGA | ||||
| GLIS family zinc finger 2 | GLIS2 | 84662 | S | CCGCTGTCCGACCTGCAGCA | |
| A | GGCTTCTCACCTGTGTGCGACCG | ||||
| GLIS family zinc finger 3 | GLIS3 | 169792 | S | TGCTCACCAATGGGAAGCCGCG | |
| A | AGCCAAGAGCCCCTTTCCCAGGAT | ||||
| Zinc finger and SCAN domain containing 4 | ZSCAN4 | 201516 | S | TCCACCTGCCTTAGTCCACGTCCA | |
| A | TGGGAGGGTGTCCCCATGTTTGCT | ||||
| Internal control | |||||
| Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | 2597 | S | CCACTTTGTCAAGCTCATTTCCT | |
| A | TCTCTTCCTCTTGTGCTCTTGCT | ||||
| Bisulfite genomic sequencing PCR | |||||
| Nanog homeobox promoter | Bis-NANOG P | 79923 | S | GTTGGGTTTGTTTTTAGGTTTT | |
| A | CATAAAACAACCAACTCAATCC | ||||
| POU class 5 homeobox 1 promoter | Bis-OCT3/4 P | 5460 | S | GTTAAGGTTAGTGGGTGGGATT | |
| A | AACATAAAAAAATCCCCCACA | ||||
| Methylation-specific PCR | |||||
| Unmethylated-XIST promoter | Unmet-XIST P | 7503 | S | TTTTGTTGTAGTGTTTAAGTGGT | |
| A | AACCCACCATATTTTACACTACA | ||||
| Methylated-XIST promoter | Met-XIST P | 7503 | S | TGTCGTAGTGTTTAAGTGGC | |
| A | CCGCCATATTTTACACTACG |
S, sense primer; A, antisense primer.