Epigenetic states and expression of imprinted genes in human embryonic stem cells

Table 1 Polymerase chain reaction primer sequences and polymorphisms

Gene	Primer sequence (5'→3')	Size (bp)	SNP	Acc. NoLocation	Ref.
IGF2	F CTTGGACTTTGAGTCAAATTGG	235	G→A	X07868	[18]
	R CCTCCTTTGGTCTTACTGGG			Pos. 820
IPW	F GGGAACTCTTCTGGGAGTGAATGTTATCA	1550	C→T	U12897	[18]
	R GGGAGGTTCATTGCACAGAAATTTGG			Pos. 1670
	Seq. TGGATAGATGCACACAAACAC	868
NESP55 gDNA	F GGCTCCTTGTGCTGTCTGTCTTGTAG	233	T→C	M21741	[18]
	R CCACACAAGTCGGGGTGTAGCTTA			Pos. 299
NESP55 cDNA	F TCGGAATCTGACCACGCGCA	1141
	R CACGAAGATGATGGCAGTCAC
	Seq. CAACCTGAAAGAGGCGATTGAA
PEG10	F TCATTTTCCTGCCTGGTTGC	405	C→T	XM_496907	[19]
	R GGAGCCTCTCATTCACAGC			Pos. 4404
KCNQ1 gDNA	F CACTGCCTGCACTTTGAGCC	282	G→A	AJ006345	[19]
	R GTGAGGAGAAGGGGGTGGTT			Pos. 331010
KCNQ1 cDNA	F GGACCTGGAAGGGGAGACT	282
	R GCGATCCTTGCTCTTTTCT
ATP10A	F AAAGACACCACCGACAGGAA	318	G→C	BC052251	This study
	R ATGCTCATGTCCACTGTGCT			Pos. 4006
TCEB3C	F CCAGAGCTGAGAGAAAGTGC	249	C→G	NM_145653	This study
	R TTTCCTGGCGAGACGATTTG			Pos. 772

gDNA: Genomic DNA; SNP: Single nucleotide polymorphism.

Table 2 Allele-specific expression of imprinted genes in human embryonic stem cell lines

Genes	hESC lines	gDNA	cDNA
			Undiff. cells	Tetratoma	EB
IPW	T1	T/C	T	T
	T2	T/C	T	T
PEG10	T2	C/T	C	C
	T3	C/T	C
NESP55	T1	T/C		T
KCNQ1	T3	G/A	G
ATP10A	T2	C/G	C	C
TCEB3C	T1	G/C		G
IGF2	T2	A/G	A	A
	T3	G/A	G > Aa
	T4				A/Gb

^aIndicates partially expressed A allele; ^bDenotes bi-allelic expression. gDNA: Genomic DNA; EB: Embryoid bodies.

Table 3 Expression of 32 human imprinted genes

Genes	T1	T2	T3	T4	T5	EB4	TT1	Probe ID	Chromosome	Exp. allele
GRB10	2543	3249	3128	3778	5927	68	96	209409_at	7p12-p11.2	P/M
PEG10	1602	1080	1710	2033	3255	1330	683	212094_at	7q21	P
SGCE	1256	1620	1725	751	501	250	737	204688_at	7q21-q22	P
MEST	7066	7416	2609	8727	581	48	28	202016_at	7q32	P
SDHD	2702	4707	2324	4849	4079	104	235	202026_at	11q23	P
SNRPN	4819	3228	6721	5534	5934	2895	1571	228370_at	15q11.2	P
SNURF	42361	58257	27211	64033	57468	11	159	201522_x_at	15q11.2-q12	P
NDN	458	932	734	734	334	8	49	209550_at	15q11.2-q12	P
IPW	2653	2848	1842	4685	8969	113	328	213447_at	15q11-q12	P
GNAS-NESP55	30303	49688	45911	55643	46465	66	905	212273_x_at	20q13.3	M
UBE3A	4119	2012	3125	2362	4491	7812	6646	211285_s_at	15q11-q13	M
HYMAI	60	196	76	16	110	113	401	215513_at	6q24	P
PLAGL1	35	12	22	5	18	79	235	1559282_at	6q24-q25	P
WT1	90	25	56	9	126	31	129	206067_s_at	11p13	P
KCNQ1DN	89	78	31	17	62	15	13	220629_at	11p15.4	M
KCNQ1	232	552	25	170	28	89	159	204487_s_at	11p15.5	M
SLC22A18	274	31	39	519	72	13	134	204981_at	11p15.5	M
PHLDA2	205	131	149	189	131	66	117	209802_at	11p15.5	M
H19	83	100	22	95	12	3	107	224997_x_at	11p15.5	M
CDKN1C	22	30	17	125	19	119	938	213183_s_at	11p15.5	M
DLK1	13	461	38	1049	8	23	32	209560_s_at	14q32	P
MEG3	38	123	215	87	12	40	10	226211_at	14q32	M
HBII-437	97	101	60	128	168	25	1091	214834_at	15q11.2-q12	P
MAGEL2	22	26	7	22	17	40	125	219894_at	15q11-q12	P
MKRN3	82	71	55	168	148	85	304	206585_at	15q11-q13	P
TCEB3C	15	135	13	5	144	49	548	1552860_at	18q21.1	M
TP73	136	62	13	62	78	1241	1058	232546_at	1p36.3	M
COPG2	50	75	15	45	106	1040	737	222298_at	7q32	P
OSBPL5	240	168	170	559	526	1210	1895	233734_s_at	11p15.4	M
IGF2	20	17	66	12	20	2596	2014	210881_s_at	11p15.5	P
ATP10A	138	248	105	198	98	134	1081	214256_at	15q11.2	M
PEG3	72	44	57	14	134	808	479	209242_at	19q13.4	P

EB4: T4 Embryoid bodies; TT1: T1 teratoma. Expression of either maternal (M) or paternal (P) allele was according to Morison et al^[16](2005).