Identification of age-related CpG sites from longitudinal avian methylomes

Sex chromosomes are thought to play an important role in sex-dependent ageing, yet they are neglected in epigenetic aging research. We identified genome-wide age-related CpG (AR-CpG) sites in two avian species (zebra finch and jackdaw) and found AR-CpG sites to be overrepresented on the haploid, female-specific W chromosome in both species, and on the Z chromosome in the zebra finch. , Zebra finch blood samples were collected during a long-term experiment where birds were housed in outdoor aviaries (320 × 150 × 210 cm) each containing single sex groups of 18–24 adults . Twenty longitudinal samples were collected from ten known-age individuals (six males and four females) sampled twice during their lifetime at an average interval of 1,470 days between the two sampling points. Jackdaw blood samples were collected from individuals of a free-ranging population breeding in nest-boxes south of Groningen, the Netherlands (53.1708°N, 6.6064°E). We analyzed 22 longitudinal blood samples collected during 2007 – 2021 from 11 known age adults (five males and six females) with an average sampling interval of 2,429 days. Samples were taken between June 2008 and December 2014 and stored in -80oC in EDTA buffer.
We extracted total-cell DNA using innuPREP DNA Mini Kit (Analytik Jena GmbH+Co) from 3μl (nucleated) red blood cells according to the manufacturer’s protocol. Whole genome se..., , # Identification of age-related CpG sites from longitudinal avian methylomes

[https://doi.org/10.5061/dryad.wm37pvmw8](https://doi.org/10.5061/dryad.wm37pvmw8)

Data for identification of age-related CpG sites from longitudinal avian methylomes

# Description of the data and file structure

## Codes:

**Code #1**: 

* Bioinformatics code for DNA methylation extraction from WGBS and EMSeq data

**Code #2:**

* Merging DNA methylation measurements per CpG site per sample in one data frame per species

- Running the initial part of the pipeline for identification of age-related CpG sites

**Code #3:**

* Functional annotation of all CpG sites captured by our analysis

**Code #4:**

* Finals steps of the pipeline

- Functional annotation of age-related CpG sites

* Statistical analyses

- Plots

## **File descriptions:**

\"**JD_AgeRelated_CpG_noMT_Final.csv**\"- Contains information for all age-related CpG sites per sample for the jackdaw.

\"Pos\": age-related CpG site position(Chromosome_p...