Table 2 Sequences of oligonucleotides used for cloning, site directed mutagenesis and ChIP
From: Non-consensus GLI binding sites in Hedgehog target gene regulation
Usage | Primer | Sequence (5'-3') |
|---|---|---|
PTCH1_WT cloning | Â | Â |
| Â | Prom_PTCH1_fw | GCAGGTCGACACACTGGCGCACTATCCAG |
| Â | Prom_PTCH1_rv | ACGAGGATCCGCTCCGGTTGACAGACCA |
PTCH1_WT mut | Â | Â |
| Â | PTCH1_mBS1_fw | GCCGGACCT GG CA GTATTTGCTGC |
| Â | PTCH1_mBS1_rv | CAAATACTG CC AGGTC CGGCTCGC |
| Â | PTCH1_mBS2_fw | GGTTGCCTACCTG CC TGGTC TCTCT |
| Â | PTCH1_mBS2_rv | AAGTAGAGAGACCA GG CA GGTAGGC |
| Â | PTCH1_BS2-3T_fw | CACACACTGGGTTGCCTACCTGGGTG A TC TCTCTACTTTGGTGAGC |
| Â | PTCH1_BS2-3T_rv | GCTCACCAAAGTAGAGAGA T CACCCA GGTAGGCAACCCAGTGTGTG |
| Â | PTCH1_BS2-8A_fw | CACACACTGGGTTGCCTACCT T GGTGGTC TCTCTACTTTGGTGAGC |
| Â | PTCH1_BS2-8A_rv | GCTCACCAAAGTAGAGAGACCACC A A GGTAGGCAACCCAGTGTGTG |
PTCH1_VAR cloning | Â | Â |
| Â | pGL3_PTCH1_vs_fw1 | AATAGGCTGTCCCCAGTGC |
| Â | pGL3_PTCH1_vs_rv1 | TAGAATGCATGGTAGGCAACCCAGTG |
| Â | pGL3_PTCH1_vs_fw2 | ATTACTCGAGTCTCTACTTTGGTGAGCTG |
| Â | pGL3_PTCH1_vs_rv2 | GTCTTCCATGGTGGCTTTACC |
| Â | Linker_fw | TTTGAATTCCGGACCACCCAAC |
| Â | Linker_rv | TCGAGTTGGGTGGTCCGGAATTCAAATGCA |
Inserted oligos*; | Â | Â |
| Â | Cons_fw | TTTAAGCTTCGTGGGTGGTC AC |
| Â | Cons_rv | TCGAGTGACCACCCA CGAAGCTTAAATGCA |
Gli1_Prom mut | Â | Â |
| Â | GLI1_mBS_Cons_fw | GTTTGCGCTTCTCGT G GGTGGTC CGGGCTTGCGGCCCGGCGG |
| Â | GLI1_mBS_Cons_fw | CCGCCGGGCCGCAAGCCCGGACCACC C A CGAGAAGCGCAAAC |
JUN_Prom mut | Â | Â |
| Â | JUN_mBS3_Cons_fw | CTTCGGAGTGTTCTCAACGTGGG T GG T C GACTCTCGGGAGACCGC |
| Â | JUN_mBS3_Cons_rv | GCGGTCTCCCGAGAGTCG A CC A CCCA CGTTGAGAACACTCCGAAG |
PTCH BS2 ChIP | Â | Â |
| Â | ChIP_PTC_BS2_fwd | GAGGATGCACACACTGGGTTGCCTA |
| Â | ChIP_PTC_BS2_rev | GGGCTGTCAGATGGCTTGGGTTTCT |
TGM3 ChIP | Â | Â |
| Â | ChIP_TGM3_BS1_fw | AGAGGGGTGGGAGTGATTATC |
| Â | ChIP_TGM3_BS1_rv | AAGAAACGTCTCAGCAGAACC |
| Â | ChIP_TGM3_B_fw | AGGTCATTGAAAGGAGTGCCCG |
| Â | ChIP_TGM3_B_rv | ATGACTAAGAAAAGAGCAGAGGG |