DNA methylation data for the PNAS paper: https://doi.org/10.1073/pnas.2515183123

Genomic DNA was extracted from approximately one million cells per condition (QIAamp DNA Blood Mini Kit, 51104). The genomic DNA was then brought to the Stanford Genomics Facility, where bisulfite conversion and methylation chip experiments using the Infinium MethylationEPIC Kit were conducted. For quantification of the methylation data, the methylclock package(6) was used. There were technical replicates for the control samples (CRA NT, CRI NT). Due to a small fraction of CpG islands having inconsistent methylation rates between repeats, these repeats had about 15 - 30 % variability in methylation clock results. To correct for this technical variation, for each CpG island, the difference of the repeats was divided by the mean of the repeats, and only those CpGs with less than 15 % variability were kept. The more variable CpGs were filtered out, meaning they did not contribute to the methylation clock calculations. The specific CpGs filtered out for CRA NT were also filtered out for CRA EZH2 and CRA E2F3; the CpGs filtered out for CRI NT were also filtered out for CRI STAT3 and CRI ZFX. Then, the mean value for the technical repeats was calculated.