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 |