Sequencing method matters: Differential performance of DNA methylation data acquisition in epigenetic clock calibration

Age is an important trait, influencing an individual’s physiology, behavior, and survival probability. Epigenetic clocks offer a mechanism to estimate ages by generating accurate age estimates based on DNA methylation at particular CpG sites, which changes in a predictable manner over lifespan. Here, we compared the efficacy of two DNA methylation sequencing methods, whole genome enzymatic methyl sequencing (WGEM-seq) and epiRADseq, in calibrating epigenetic clocks for chestnut-crowned babbler (Pomatostomus ruficeps) nestlings (N = 56, aged 0-19 days). Epigenetic clocks using WGEM-seq data outperformed clocks using epiRADseq data, indicating that the lower resolution of epiRADseq does not allow for accurate clock calibration. Using WGEM-seq  data collected throughout a small fraction of the lifespan of chestnut-crowned babblers, we successfully calibrated a highly accurate epigenetic clock. These results open promising avenues for investigating the impact of early life environments..., , # Sequencing method matters: Differential performance of DNA methylation data acquisition in epigenetic clock calibration

Dataset DOI: [10.5061/dryad.0cfxpnwfc](10.5061/dryad.0cfxpnwfc)

## Description of the data and file structure

Chestnut crowned babblers of known ages were bled between 0 and 2000 days old. DNA was extracted from blood samples and epiRADseq or whole genome enzymatic methylation was used to determine methylation of sites throughout the genome. Methylation was then used to generate epigenetic clocks.

For both files, individual ID is listed in the header of each column, age in days is in the second row, and every value below that is the methylation at a particular CpG site for that individual.

### Files and variables

#### File: epiRAD.csv

**Description:** Data used to generate epigenetic clock with epiRADseq data.

#### File: EMseq.csv

**Description:** Data used to generate whole genome enzymatic methylation data.

## Code/software

Both files are .csv files and ...,