SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells

Toghill, Bradley J.; Saratzis, Athanasios; Freeman, Peter J.; Sylvius, Nicolas; Bown, Matthew J.

doi:10.1186/s13148-018-0460-9

Table 1 Candidate genes and amplicons for VSMC bisulphite NGS: Genomic locations, primer sequences, annealing temperatures and CpG coverage are displayed for each amplicon targeting candidate genes

From: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells

Gene symbol	Chromosome and RefSeq ID	RefSeq ID coordinates	Primer sequence 5′-3’	Annealing temp (°C)	CpG coverage
LRP1		3875–4240	F: TAGAAGGGGGTAGTGATTAAAAGTA	54	13
		3875–4240	R: AAAACAAACCCTAATTTAAAAAAAA	54	13
	Chr: 12	4274–4640	F: GGGTATTAAGGTGGGTTTTATTTT	57	25
	NG_016444.1	4274–4640	R: TACTCTAAAATTTCAAACTCCCTCC	57	25
		4680–5036	F: GTATTAGGGAGGAGGGTTTAGTTAG	54	24
		4680–5036	R: TCCTCAATACATAAACCTAAAACTC	54	24
ERG		282787–283319	F:TTTTATTAGGTAGTGGTTAGATTTAGTTTT	54	22
	Chr: 21	282787–283319	R: TACCCCCAATTAATAAATTCCAATATA	54	22
	NG_029732.1	283331–283680	F: TTGGAATTTATTAATTGGGGGTATATAT	57	6
		283331–283680	R: ACACTATCTTTTACAAAATCAATCCAC	57	6
		5162–5540	F: AAAATTTTTGGAAGGGGTTTAGTT	56	37
		5162–5540	R: ATAATATTTTTCCAACCTCATTAAAAAC	56	37
MMP-9		3980–4579	F: TTGGGTTTAAGTAATTTTTTTATTT	52	7
	Chr: 20	3980–4579	R: TAACCCATCCTTAACCTTTTACAAC	52	7
	NG_011468.1	4640–5600	F: GATGGGGGATTTTTTTAGTTTTATT	57	8
		4640–5600	R: TACCCATTTCTAACCATCACTACTC	57	8
LDLR		4376–4725	F: TTTTTTAAGGGGAGAAATTAATATTTA	54	5
		4376–4725	R: CACAAAAAAATAACAACAACCTTTC	54	5
		4776–5355	F: GAAAGGTTGTTGTTATTTTTTTGTG	57	28
	Chr: 19	4776–5355	R: AAACTCCCTCTCAACCTATTCTAAC	57	28
	NG_009060.1	5464–5972	F: TTTAAGTTTTTATAGGGTGAGGGAT	56	31
		5464–5972	R: ACACCCAACTCAAAATAACAATAAC	56	31
		6054–6785	F: AATTTTATTGGGTGTAGTTTAATAGGTTAT	54	49
		6054–6785	R: CTCAAAATCATACACTAACCAACCTC	54	49
IL6R		2781–3061	F: TTTTTGTTTAGGTTGGAGTGTAGTG	52	8
	Chr: 1	2781–3061	R: CAAAATTTTAATATTATAATTCACATAAAA	52	8
	NG_012087.1	3095–3729	F: GTTTGTTTTGGTGTAGAGATAGGTG	58	7
		3095–3729	R: ATAAAACTCCCAAATAAACAAAACC	58	7
SORT1	Chr: 1	4363–4804	F: AGATTATTTTTTAGGTTTGTAGGAGTTA	55	24
SORT1	NG_028280.1	4363–4804	R: AACAAAAACTACTAAAATCAACCCC	55	24
SMYD2		214280141–214280630	F: TTTTATTTTGAAGTAGTGGTTTTTGTTAA	55	13
		214280141–214280630	R: TTTTCCAAAATTAAAAATTTTTAAACCT	55	13
	Chr: 1	214280631–214281330	F: AAGGTTTAAAAATTTTTAATTTTGGAAA	58	82
	NC_000001.11	214280631–214281330	R: AAATCCCCCACCTAAAAAAACTAC	58	82
		214281331–214281733	F: TTTTTTTAGGTGGGGGATTT	55	46
		214281331–214281733	R: CCCACATTTAAAAACAAAAACCTAC	55	46
SERPINB9		2891544–2892079	F: GGTGTTGAAAATATTTTTGGAGGTA	57	26
		2891544–2892079	R: AAAATCTACCATTCATCAAACTAACAAA	57	26
		2890564–2891263	F: TTAGAGGGTGGGATTAGAGGTAGTT	54	9
	Chr: 6	2890564–2891263	R: TTTCCACCTAAAAAACCAAAATTAA	54	9
	NC_000006.12	2889934–2890423	F: GTATTTGGGAATTGTTGATGTTTTT	55	11
		2889934–2890423	R: ACAACAAAAAATCATTATAATCTATTTTCT	55	11
		2889425–2889933	F: AGAATTTTATATGTAATTTATTTTGG	54	31
		2889425–2889933	R: TATAATCCCAACACTTTAAAAAACC	54	31
DAB2IP		121689899–121690502	F: TTGGAGTAGTTTGTTTGTTGTGTT	57	10
		121689899–121690502	R: TAAAAAATTAAATACCCAAAACCTC	57	10
		121690573–121691062	F: TTGTTATATTTTAAGTTGAGATTTTGGG	57	6
	Chr: 9	121690573–121691062	R: TAACCACATAAAAACATTCCAAACA	57	6
	NC_000009.12	121767430–121767872	F: GGAGAGGAGATAGGAAAGTTTTTAG	57	6
		121767430–121767872	R: CTAACCTTATCCCTTACAACCACTAC	57	6
		121768273–121768692	F: AATGGAGTGGGAGTTTGTTATAGTG	57	11
		121768273–121768692	R: TAATAACAACTTTTAACCCCACCTC	57	11

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ISSN: 1868-7083

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