Table 4.

Minimal methylation was detected by using bisulfite sequencing in 8 of the 12 clones selected for bisulfite sequencing. A) Shown here is the percent cytosine methylation at the CpG dinucleotides in the liver DNA, sperm DNA, and in vivo-produced blastocyst DNA for the regions analyzed by using bisulfite sequencing in clones CC C1, EEE D4, EE A11, K D3, L E8, O D10, QQ E4, and S E3. B) Bisulfite analysis data and the microarray analysis data are in agreement for 37.5% (6/16) of the samples (shown in bold type). The ratios produced from the microarray and bisulfite analysis were classified as consistent when the bisulfite analysis-produced ratio indicated the sample was hypomethylated (>1) or hypermethylated (<1) and matched the methylation status of the microarray-produced data. From the microarray-produced ratios, the samples were classified as hypermethylated when the ratio was < 0.8 and the sample was classified as hypomethylated when the ratio was >1.2. The ratios produced from bisulfite analysis data and the microarray analysis data are not in agreement for 62.5% (10/16) of the samples (shown in parentheses). The microarray values are LOWESS normalized Cy5/Cy3 ratios representing the methylation status of the specified clones in the liver (Cy5) and in vivo-derived blastocyst (Cy3) samples. The Bisulfite ratios (Ref/Sample) were calculated from the equation shown in the Materials and Method section.

A
	Percent methylation
	Liver	Sperm	IVP Blast
CC C1	0.00	0.00	1.54
EE A11	0.00	0.00	1.43
EEE D4	0.00	1.56	1.10
K D3	0.62	0.00	0.00
L E8	0.00	0.00	7.14
O D10	1.24	2.14	4.76
QQ E4	0.00	0.00	2.22
S E3	6.92	3.00	7.50
B
Sperm (Ref/Sample)		IVP Blast (Ref/Sample)
Bisulfite	PDMH microarray	Bisulfite	PDMH microarray
(1.000)	(2.055)	(0.985)	(0.375)
(1.000)	(1.262)	(0.986)	(0.173)
0.984	1.074	(0.989)	(32.960)
(1.006)	(0.593)	(1.006)	(2.806)
1.000	1.033	(0.929)	(0.464)
0.991	1.105	(0.964)	(6.897)
(1.000)	(0.462)	0.978	1.135
1.042	0.910	0.994	0.859