Table 3.
Primers for PCR analyses
| Primer pair | Sequence | Use |
| TIMP1 5' (promoter) [14] | 5'A: CCCTTGGGTTCTGCACTGA* 5'B: CCAAGCTGAGTAGACAGGC |
Methylation ChIP DNase sensitivity |
| TIMP1 CA (gene body) [12] | CA1: GGGTTCCAAGCCTTAGGGGA CA2: AGGCTGTTCCAGGGAGCCGC |
DNase sensitivity |
| TIMP1 S (bisulfite) | 5S: GttttTTGGtTTtTGtAtTGATGGT 3S: CCAAaCTaAaTAaACAaaCATCTAaC** |
Bisulfite sequencing |
| ARAF1 M1:M4 (promoter) [14] | M1: TGCCAAAGCCCTAAGGTCA M4: CGCTGTCGACGATGGTCT M3: GTGAGGAAACAAGAAGAGAG |
Methylation ChIP DNase sensitivity |
| XIST 3':5' (gene body) [39] | 3':GAAGTCTCAAGGCTTGAGTTAGAAG 5': TTGGGTCCTCTATCCATCTAGGTAG |
Methylation DNase sensitivity |
| XIST A5:29r (promoter) [37] | A5: TTTCTTACTCTCTCGGGGCT 29r: ATCAGCAGGTATCCGATACC |
ChIP |
| ELK1 5' (promoter) [14] | A: GCACAGCTCTGTAGGGAA B: AGCTCACCTGTGTGTAGCG |
Methylation ChIP |
| STA A:B (intergenic) | A: CACCTGTGTGTCATGTATAC B: CCAGTATTGGTCTTCCAGTT |
DNase sensitivity |
| 8037 A:B (intergenic) | A: GAGGCAAGACATCCATTCC B: TGACTTTGAGCGAGCAGGT |
Reference region |
* There is a mismatch in the TIMP 5'A primer, the underlined G should be C.
** The lower-case letters in the primers are the bases modified by the bisulfite reaction. All C nucleotides should have been converted because there were no CpG pairs with possible protective methylation.