Winner 2024 - Identification of age-related CpG sites from longitudinal avian methylomes

Open Research objectives/practices

Before even submitting our paper, we have made available our raw data as well as the bioinformatic and statistical codes used to identify age-related sites in longitudinal avian methylomes.

Introduction

Our aim is to provide a detailed, clean, reproducible dataset for identification of age-related CpG sites from longitudinal avian full methylomes. Making such a dataset and code publicly accessible not only promotes transparency and scientific integrity but also provides a valuable resource for scientists looking to conduct similar analyses, allowing them to use our work as a foundation.

Motivation

Epigenomic data require extensive pre-processing and analysis in order to extract useful information from raw sequences. When I started my PhD, despite the abundance of papers on the topic, the associated code and data were rarely shared. Additionally, the Methods sections of these papers often lacked sufficient detail, making it difficult for readers to reconstruct the analysis steps that led to the reported results.

Lessons learned

Due to the large volume of the data and the extensive documentation required to save and share all variables, making this dataset publicly available was a tedious and time-consuming process. However, our commitment to transparency, scientific integrity, and reproducibility made it worthwhile. We hope that more scientists working with similar data will follow our example and share their analyses in detail.

URLs, references and further information

• https://doi.org/10.5061/dryad.wm37pvmw8