Table 3.
List of PCR primers used in this study. Primer sequences (F, forward; R, reverse) are represented (5´to 3´orientation) for promoter and coding regions of active and inactive genes. Primers designed for the Polr2a locus (scheme in Figure 5—figure supplement 1a) cover the promoter region (–1 and –0.5 kb), exons (E1 and E28), intron (I1), exon-intron boundaries (I2/E3 and E19/I19) and downstream of TES (+2 kb TES).
| Gene | Primer sequence | Gene | Primer sequence |
|---|---|---|---|
| ChIP primers β-actin (promoter) F |
GCAGGCCTAGTAACCGAGACA |
Gene expression primers β-actin 5´F |
CCACCCGCGAGCACA |
| β-actin (promoter) R | AGTTTTGGCGATGGGTGCT | β-actin 5´R | CCGGCGTCCCTGCTTAC |
| β-actin (coding) F | TCCTGGCCTCACTGTCCAC | β-actin Exon1 F | TCTTTGCAGCTCCTTCGTTG |
| β-actin (coding) R | GTCCGCCTAGAAGCACTTGC | β-actin Exon2 R | ACGATGGAGGGGAATACAGC |
| Oct4 (promoter) F | GGCTCTCCAGAGGATGGCTGAG | Oct4 5´F | TGAGCCGTCTTTCCACCA |
| Oct4 (promoter) R | TCGGATGCCCCATCGCA | Oct4 5´R | TGAGCCTGGTCCGATTCC |
| Oct4 (coding) F | CCTGCAGAAGGAGCTAGAACA | Sox2 5´F | AGGGCTGGGAGAAAGAAGAG |
| Oct4 (coding) R | TGTGGAGAAGCAGCTCCTAAG | Sox2 5´R | ATCTGGCGGAGAATAGTTGG |
| Myf5 (promoter) F | GGAGATCCGTGCGTTAAGAATCC | Serpine1 5´F | CCCCGAGAGCTTTGTGAAG |
| Myf5 (promoter) R | CGGTAGCAAGACATTAAAGTTCCGTA | Serpine1 5´R | AAGGTGCCTTGTGATTGGCT |
| Myf5 (coding) F | GATTGCTTGTCCAGCATTGT | Dusp1 5´F | CGGTGAAGCCAGATTAGGAG |
| Myf5 (coding) R | AGTGATCATCGGGAGAGAGTT | Dusp1 5´R | AGGAGCGACAATCCAACAAC |
| Gata1 (promoter) F | AGAGGAGGGAGAAGGTGAGTG | Ctgf 5´F | GACTCAGCCAGATCCACTCC |
| Gata1 (promoter) R | AGCCACCTTAGTGGTATGACG | Ctgf 5´R | GTGCAGAGGCGACGAGAG |
| Gata1 (coding) F | TGGATTTTCCTGGTCTAGGG | ||
| Gata1 (coding) R | GTAGGCCTCAGCTTCTCTGTAGTA | ||
| Polr2a (-1 kb) F | CCGTAAAGCTATTAGAGCACAGG | ||
| Polr2a (-1 kb) R | ATGCATAAGGCAGGCAAGAT | ||
| Polr2a (-0.5 kb) F | GTAACCTCTGCCGTTCAGGA | ||
| Polr2a (-0.5 kb) R | TTTCTCCCTTTCCGGAGATT | ||
| Polr2a (E1) F | CAGGCTTTTTGTAGCGAGGT | ||
| Polr2a (E1) R | GACTCAGGACTCCGAACTGC | ||
| Polr2a (I1) F | CAGAGGGCTCTTTGAATTGG | ||
| Polr2a (I1) R | GCATCAGATCCCCTTCATGT | ||
| Polr2a (I2/E3) F | GCCCTCTTCTGGAGTGTCTG | ||
| Polr2a (I2/E3) R | AGGAAGCCCACATGAAACAC | ||
| Polr2a (E19/I19) F | CCAAGTTCAACCAAGCCATT | ||
| Polr2a (E19/I19) R | TCTTAACCGCTGAGCCATCT | ||
| Polr2a (E28) F | TCTCCCACTTCTCCTGGCTA | ||
| Polr2a (E28) R | CCGAGGTTGTCTGACCCTAA | ||
| Polr2a (+2 kb TES) F | GAGGGGCAGACACTACCAAA | ||
| Polr2a (+2 kb TES) R | AAAAGGCCAAAGGCAAAGAT |