Fig. 3

Analysis of CpG methylation in established and novel aging associated loci. A–F Analysis of CpG methylation status of selected Stubbs Loci (see Table 2) in LDC (over Co) mice from liver hepatocytes (using RRBS) and in bulk liver (using SNuPE). The CpG methylation is compared to bulk liver from aging mice using SNuPE and MiSeq. G, H The CpG methylation of the new aging loci was also measured in LDC (over Co) mice and compared to aging bulk liver using SNuPE and MiSeq. t test (parametric, unpaired) was used to compare and evaluate the significance between groups Co vs LDC and young (Y = 10 wks), mid-aged (MA = 40 wks) vs aged (A = 85 wks) for each of the technologies, in female mice. All differences that are significant (* p < 0.05) are marked in the plot. In each case, comparisons were made only between two groups (LDC vs. Co, Y vs. A or Y vs. MA for each technology). The gene associated with the measured CpG is mentioned at the bottom of each plot. The source of the sample and their age are mentioned on top. For better comparison, methylation index values obtained from SNuPE analyses were normalized to the range of [0,100]. RRBS data was excluded when read coverage for the respective CpG was below 3 (concerns Smarca2, Inpp5a). SNuPE analysis of CpGs with low read coverage were excluded