Max Planck Institute for Evolutionary Biology
Published January 13, 2023 | Version 0.0.1
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Sex-specific changes in autosomal methylation rate in ageing common terns - Code

Creators

  • 1. Max-Planck-Society

Contributors

  • 1. Max-Planck-Society
  • 2. Institute of Avian Research

Description

In the manuscript "Sex-specific changes in autosomal methylation rate in aging common terns" published in Frontiers Ecology And Evolution, we investigate sex-specific age effects in global DNA methylation patterns in aging common terns in a longitudinal study. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome.

The raw RRBS reads can be found at: https://www.ebi.ac.uk/ena, PRJEB48910 and the genome at https://www.ncbi.nlm.nih.gov/, PRJNA560234. 

This document combines the various scripts and programs used for the Reduced Representative Bisulfite Sequencing data analyses and GLMMs (e.g. RefFreeDMA, picard, bismark, and R) into one combined script to make the work reproducible. We further share the final data frame used for the GLMM under another DOI: 10.5281/zenodo.7533890. 

 

 

 

Notes

Note: For more information regarding further (meta) data or analyses, please contact sandra.bouwhuis@ifv-vogelwarte.de or britta@bsmeyer.com. Please also contact sandra.bouwhuis@ifv-vogelwarte.de if you'd like to use the shared data. These data are part of those collected in an ongoing individual-based longitudinal population study and additional data are likely to be available, and we are generally happy to collaborate, provided that none of our own staff or students is working on a conflicting project. Funding: This study was supported by the Max Planck Society through a MPRG grant (MFFALIMN0001 to ML), a sequencing grant (PSLIMN6000 to ML and SB), and the "Norddeutscher Wissenschaftspreis 2018" (to BM, SB and ML).

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Additional details

Related works

Compiles
Dataset: 10.5281/zenodo.7533890 (DOI)
Is published in
Journal article: 10.3389/fevo.2023.982443 (DOI)