/BrainZoo

Scripts used in brain mCH manuscript

Primary LanguageRMIT LicenseMIT

BrainZoo

Files and code used for de Mendoza, A., Poppe, D., Buckberry, S. et al. "The emergence of the brain non-CpG methylation system in vertebrates". Nat Ecol Evol (2021). https://doi.org/10.1038/s41559-020-01371-2

Code

  • MasterScript_BrainZoo.R
  • ATCGmap_GenotypeCorrector.sh

Files

  • DNMT3.phylogeny: Amino acid sequence alignments and phylogeny of DNMT3 orthologues.
  • MECP2_MBD4.phylogeny: Amino acid sequence alignments and phylogeny of MECP2/MBD4/MBD1-2-3 orthologues.
  • Kallisto_brain_samples.tar.gz: Kallisto output files for brain RNA-seq samples for every species.
  • mCH_stats.tsv: Global mCH levels for each brain WGBS sample.
  • all_GOs_simplified.csv.gz: gProfiler Gene Ontology lists for each species divided by top mCA, bottom mCA, top mCG, bottom mCG.