Table 1 Variability of LINE-1 methylation levels of DNA from cryo-preserved tissue
converted DNA samples | PCR 1 (% of methylation) | PCR 2 (% of methylation) | SD due to different PCR and different pyrosequencing | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
pyrosequencing 1 | pyrosequencing 2 | pyrosequencing 1 | pyrosequencing 2 | |||||||||||||
CpG site 1 | CpG site 2 | CpG site 3 | CpG site 1 | CpG site 2 | CpG site 3 | CpG site 1 | CpG site 2 | CpG site 3 | CpG site 1 | CpG site 2 | CpG site 3 | CpG site 1 | CpG site 2 | CpG site 3 | ||
A1 | 55.9 | 62.9 | 62.3 | 55.0 | 62.1 | 62.2 | 56.5 | 61.6 | 59.3 | 54.6 | 63.4 | 61.4 | 0.9 | 0.8 | 1.4 | mean = 0.9 |
A2 | 53.1 | 63.1 | 59.7 | 56.0 | 63.3 | 59.5 | 53.2 | 62.7 | 60.0 | 57.5 | 62.3 | 60.5 | 2.2 | 0.4 | 0.4 | |
A3 | 55.7 | 61.9 | 58.6 | 55.4 | 61.8 | 61.1 | 54.8 | 60.6 | 59.6 | 55.3 | 62.5 | 61.6 | 0.4 | 0.8 | 1.4 | |
A4 | 54.1 | 63.8 | 60.7 | 56.4 | 63.6 | 59.9 | 56.4 | 63.7 | 60.3 | 55.8 | 64.1 | 59.6 | 1.1 | 0.2 | 0.5 | |
B1 | 56.3 | 61.8 | 62.7 | 57.8 | 63.1 | 63.5 | 58.0 | 62.9 | 60.6 | 56.7 | 64.1 | 61.4 | 0.8 | 0.9 | 1.3 | |
B2 | 55.9 | 63.4 | 62.9 | 57.9 | 64.0 | 63.2 | 55.2 | 63.1 | 62.5 | 58.6 | 64.7 | 63.3 | 1.6 | 0.7 | 0.4 | |
bisulfite-to-bisulfite SD | 1.3 | 0.8 | 1.8 | 1.2 | 0.9 | 1.7 | 1.7 | 1.1 | 1.1 | 1.5 | 0.9 | 1.2 | ||||
mean = 1.3 | ||||||||||||||||
SD between all measures of site 1 | 1.4% | |||||||||||||||
SD between all measures of site 2 | 1.0% | |||||||||||||||
SD between all measures of site 3 | 1.4% | |||||||||||||||