. 2014 May 27;133(8):1059–1073. doi: 10.1007/s00439-014-1447-z

Table 1.

List of primers and probes used in this study

Method	Primer sequence
Pyrosequencing
CpG island	FP: 5ʹ-TGTGTTAAGTTGTTTAGGGGTTTTA-3ʹ
	RP: 5ʹ-ACTACAATCTCTACCTCCCAAATTC-biotin-3ʹ
	SP: 5ʹ-AATATTATGTGGGAAATTGT-3ʹ
5ʹUTR	FP: 5ʹ-TTGGAGTATATAGGTAGTATTA-3ʹ
	RP: 5ʹ-TCCCCTAAAATCTCTAAC-biotin-3ʹ
	SP: 5ʹ-TTAGTTGTGTAGGAGAAAGG-3ʹ
GDF5 expression	FP: 5ʹ-CTGTGATTCCAGGAGTGCAG-3ʹ
	RP: 5ʹ-ATCCTCTTCATTGACTCTGCC-3ʹ
	Pr: 5ʹ-CCACGACCATGTCCTC-3ʹ
rs143383 genotyping	FP: 5ʹ-AGTCAGTTGTGCAGGAGAAAGG-3ʹ
	RP: 5ʹ-GCAGCTGAAAATAACTCGTTCTTGAA-3ʹ
	Pr: 5ʹ-AGAAAGCCACCGCC-3ʹ
DY-682 EMSA probes
rs143383 C allele unmethylated	FP: 5ʹ-GAGAAAGGGGGCGGTCGGCTTTCTCC-3ʹ
rs143383 C allele unmethylated	RP: 5ʹ-GGAGAAAGCCGACCGCCCCCTTTCTC-3ʹ
rs143383 C allele methylated	FP: 5ʹ-GAGAAAGGGGGC^meGGTCGGCTTTCTCC-3ʹ
rs143383 C allele methylated	RP: 5ʹ-GGAGAAAGCCGACC^meGCCCCCTTTCTC-3ʹ
rs143383 T allele unmethylated	FP: 5ʹ-GAGAAAGGGGGCGGTTGGCTTTCTCC-3ʹ
rs143383 T allele unmethylated	RP: 5ʹ-GGAGAAAGCCAACCGCCCCCTTTCTC-3ʹ
rs143383 T allele methylated	FP: 5ʹ-GAGAAAGGGGGC^meGGTTGGCTTTCTCC-3ʹ
rs143383 T allele methylated	RP: 5ʹ-GGAGAAAGCCAACC^meGCCCCCTTTCTC-3ʹ
SP1/SP3 consensus competitor	FP: 5ʹ-AATTGGGGGGGCGGGGGTACGTAGCA-3ʹ
SP1/SP3 consensus competitor	RP: 5ʹ-TGCTACGTACCCCCGCCCCCCCAATT-3ʹ
Cloning into pGL3-enhancer	FP: 5ʹ-GGGGACTAGTGGATTCAAAACTAGGGGG-3ʹ
Cloning into pGL3-enhancer	RP: 5ʹ-GGGGAAGCTTCCGCTGAATGACACCAAAG-3ʹ
Cloning into EGFP-N1
SP1	FP: 5ʹ-GGGGGAATTCATGGATGAAATGACAGCTGTG-3ʹ
SP1	RP: 5ʹ-GGGGCCGCGGGAAGCCATTGCCACTGATATT-3ʹ
SP3	FP: 5ʹ-GGGGGAATTCATGACCGCTCCCGAAAAGCCC-3ʹ
SP3	RP: 5ʹ-GGGGCCGCGGCTCCATTGTCTCATTTCCAGA-3ʹ

The bold and underlined bases in the EMSA probes indicate the position of rs143383. The series of underlined bases in the SP1/SP3 competitors indicate the site of the consensus sequence for SP1/SP3

FP forward primer, RP reverse primer, SP sequencing primer, Pr probe, me methylated