TABLE 2.
Primers and gBlocks
| SYBRGreen assay | ||
|---|---|---|
|
| ||
| Gene | Forward sequence (5′ > 3′) | Reverse sequence (5′ > 3′) |
| OTX2 | TTCGGGTATGGACTTGCTGC | GATGTCTGGGTACCGGGTCT |
| GATA4 | TCTACATGAAGCTCCACGGG | TGAAGGAGCTGCTGGTGTC |
| SOX17 | AAGGGCGAGTCCCGTATC | TTGTAGTTGGGGTGGTCCTG |
| SOX9 | GAGGAAGTCGGTGAAGAACG | ATCGAAGGTCTCGATGTTGG |
| PAX6 | TCTTTGCTTGGGAAATCCG | CTGCCCGTTCAACATCCTTAG |
| CTTNBP2 | CCCCGTGGGACTTTATGAGG | GCCTTCTTGAGGACCTGACA |
| PGK1 | TAACAAGCTGACGCTGGAC | GCAGCCTTAATCCTCTGGTT |
| TaqMan assay | ||
|
| ||
| Gene | Sequence (5′ > 3′) | |
| CFTR | AGCTGTCAAGCCGTGTTCTAGATA ATGAGGAGTGCCACTTGCAAA /56-FAM/CACACGAAA/ZEN/TGTGCCAATGCAAGTCCTT/3IABkFQ/ |
|
| PGK1 | TAACAAGCTGACGCTGGAC GCAGCCTTAATCCTCTGGTT /56-JOEN/CGACTCTCA/ZEN/TAACGACCCGCTTCC/3IABkFQ/ |
|
| ChIP-qPCR | ||
|
| ||
| Amplicon site | Forward sequence (5′ > 3′) | Reverse sequence (5′ > 3′) |
| 18s | CGGCTACCACATCCAAGGAA | GCTGGAATTACCGCGGCT |
| NARG2/ICE2 promoter | GGAAAGGGGACGCAAAGAGA | TCCTACCCCTGCTTTGCTTG |
| RNF111 promoter | CACGTACAGTTTTGGTGGCG | AGTAATGCGTCGAGAGCCAG |
| ATP6V0A4 i9/10 | AAGGTGCCAAAAATGGAGTG | AGGAGAGTTCAAGGCCAGGT |
| GRM8 promoter | CCAATCAAGCTCCAATGCCC | TGTGAGAGAAATAGCGGGCG |
| APIP promoter | TTATCTTGTGGGCTTCCCCG | AATTAGCTCCGCGGCTTACA |
| EOMES Promoter | TTTCGCCGGAATTTAGGGGG | ATGACTAATGCGCCAAGGGT |
| EHF promoter | TCCCGGTTGGTGGCTTATTG | GGCACCACGGGTGTTATCAA |
| CFTR −0.5 kb promoter | GTTCTCCCGCCGGTGG | CAGTCGCGGCCTCTCTTTAG |
| CFTR DHS10a,b | TGCTTTATTGAATGGCATTACCTCTA | AGATGCTTGTGGTAAGGGAGGAG |
| CFTR i20 | AGGATGCCAGACAGGGAGAT | ACCTTTTGCCCCTCAGCTTT |
| CFTR +15.6 kb | ATCCATTTTCTTCAAGTCTCTCTCCAT | GGAATGAGGATTGTTTATGATTTGG |
| CFTR +19.6 kb | CTGCAAGTATTTCTTGGATGCTGT | GTAACCCATTTGGCTTGAGGG |
| CFTR +21.5 kb | GGCTAGTTCCTTGACCTGAACAA | TGGAAGTTCCTCCATTTTGAATG |
| CFTR +22.6 kb | GCCAGGGAATGAGTCTTGTG | GCCTCCTGTTCTTCCCAAAT |
| CFTR +48.9 kb | GGCATCAGCCAGTCAAGGTTT | AGCAGAGGGCAAGTGGTACTT |
| +22.6 kb deletion | ||
|
| ||
| Name | Sequence (5′ > 3′) | |
| +22.6 kb 5′ gBlock | TGTACAAAAAAGCAGGCTTTAAAGGAACCAATTCAGTCGACTGGATCCGGTACCAAGGTCGGGCA GGAAGAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAAT TAGAATTAATTTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTT GGGTAGTTTGCAGTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATT TCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTTCAAGACTACTTGCACGG GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGA GTCGGTGCTTTTTTTCTAGACCCAGCTTTCTTGTACAAAGTTGGCATTA |
|
| +22.6 kb 3′ gBlock | TTGTACAAAAAAGCAGGCTTTAAAGGAACCAATTCAGTCGACTGGATCCGGTACCAAGGTCGGGCAGGA AGAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGATACAAGGCTGTTAGAGAGATAATTAG AATTAATTTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAATTTCTTGG GTAGTTTGCAGTTTTAAAATTATGTTTTAAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTC GATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTACTCACACCGTCGCCAGA GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGA GTCGGTGCTTTTTTTCTAGACCCAGCTTTCTTGTACAAAGTTGGCATTA |
|
| +22.6 kb EF | TGGCACTCTCCTTCTGTGTG | |
| +22.6 kb ER | CAGGGCATCTTCTGGCTTAC | |
| +22.6 kb IF | GCCAGGGAATGAGTCTTGTG | |
| +22.6 kb IR | ACTCATTCCCTGGCTTCCTT | |
| 4C-seq primers | ||
|
| ||
| Name | Reading primer (5′ > 3′) | Nonreading primer (5′ > 3′) |
| CFTR +22.6 kb viewpoint | TACACGACGCTCTTCCGATCTCAAA CATCCTGGTAAACCATG |
ACTGGAGTTCAGACGTGTGCTCTTCCGATCTGC ACTTATCACTAGCTAATGT |
Abbreviations: CFTR, cystic fibrosis transmembrane conductance regulator; ChIP-qPCR, Chromatin immunoprecipitation followed by qPCR; CTTNBP2, cortactin binding protein 2; OTX2, orthodenticle homeobox 2.