TABLE 1.

PCR primers used in ChIP analysis and generation of probes for hybridization

Type of primer	Clone no. or gene element	GenBank accession no.	Primer (5′-3′)		PCR fragment size (bp)	PCR cycle conditionsa (×30)
			Forward	Reverse
Microarray	6	AY457178	TGCAGGAGAAGCAATATTAT	TAGAAGAGGTAGAAGAGGAAG	278	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
	116	AY457216	AGGTTTTCAGGCTAGACAGA	TCTTCTGGTCTTCTCTGAATG	96	95°C, 30 s; 53°C, 30 s; 72°C, 20 s
	265	AY457268	TCTCAGTGGAGAAAAACTTTGC	GTCGACAAATCAGAAGCTGA	270	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
	267	AY457269	GACCTATTGAGAATGCTCACA	ATGATTGTTACCTCTCTTTG	235	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
	293	AY457285	CCACTAAACCTCCTTCTCCA	AAGAAGGCTGTAGGTGGCTGT	127	95°C, 30 s; 63°C, 30 s; 72°C, 15 s
	294	AY457286	CCAGCAAGCCCTTTAGGAACA	TACTCCTACATCCTGAAAGTG	124	95°C, 30 s; 59°C, 30 s; 72°C, 20 s
	396	AY457330	CTAATCCTTATTGTACAGGA	CATGGAAATTCTACTTTGAA	264	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
	513	AY457372	CCCTTGCTCCATCTTTTGG	GTCTGCAGAAGCACTTGAAG	94	95°C, 30 s; 53°C, 30 s; 72°C, 20 s
	717	AY457431	GACTAATATTGAAAAATGTAGC	ATAGGCATTCTGGCCTTCTGAG	190	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
	794	AY457460	AAGTATTGAATTTTAGGATT	TTGAGAACCACTGCTCTAAC	234	95°C, 30 s; 48°C, 30 s; 72°C, 20 s
	1031	AY457551	TCCTCTCGGGGTTTTCTCCA	AGGAAAAGACAAAAATAACCC	138	95°C, 30 s; 50°C, 30 s; 72°C, 20 s
For ChIP assays in HD3 cells	β-Globin insulator	E02199	GAGCTCACGGGGACAGCCCC	GATCCCGTGCCACCTTCCCC	174	94°C, 1 min; 60°C, 1 min; 72°C, 4 min
	β-Actin promoter	E02199	CGCTCCGAAAGTTTCCTTTT	AGAAAAGAAACGAGCCGTCA	238	94°C, 1 min; 60°C; 1 min; 72°C, 4 min
	CTCF exon 8	Z22605	CGAGTTTTATGATACAGAAGTGGAAG	AGTTATTTACAAGCTTGACCATTACAG	318	94°C, 1 min; 55°C, 1 min; 72°C, 4 min
For hybridization (nested)	β-Globin insulator	E02199	CCCAAAGCCCCCAGGGATGTAAT	CCCGGGCTGTCCCCGCACGCT	130	94°C, 1 min; 60°C, 1 min; 72°C, 4 min
	β-Actin promoter	E02199	CCTTTTATGGCGAGGCGGCGGCGG	GGGCGAAGGCAACGCAGCGACTCC	84	94°C, 1 min; 60°C, 1 min; 72°C, 4 min
	CTCF exon 8	Z22605	CGAGTTTTATGATACAGAAGTGGAAG	AGTTATTTACAAGCTTGACCATTACAG	301	94°C, 1 min; 55°C, 1 min; 72°C, 4 min
For ChIP assays in	N-Myc site	X00364	ACCTGACCCCCGCCCTCGTTGA	CTCTACTGGCAGCAGAGATCAT	58	95°C, 30 s; 65°C, 30 s; 72°C, 20 s
transgenic NIH 3T3	GAPDH (exon 1)	X55448	ATCATGGCAGAGCAGGTGGC	GATGCACCCATGATGATAA	122	95°C, 30 s; 58°C, 30 s; 72°C, 20 s
cells	GAPDH (promoter)	X55448	TCCTGCAATGATAGACTAG	CTGCCAAACACGTTCACAGA	158	95°C, 30 s; 55°C, 30 s; 72°C, 20 s
For ChIP assays of wt and mut H19 ICR		AF049091	TCCCTTTGGTCACTGAACC	AATCCCTATTTGGGTGACCC	319	94°C 30 s; 50°C 45 s; 72°C 50 s

^aPCR conditions for all cycles were initial denaturation, 94°C and 5 min, and final elongation, 72°C and 10 min.