Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense

This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of Thlaspi arvense, investigating the genetic and environmental drivers of epigenetic variation. 207 lines from across Europe were grown in common environment and scored for genetic and DNA methylation variation by Whole Genome Sequencing and Whole Genome Bisulfite Sequencing respectively. This repository includes (1) average methylation values for all lines and the respective processed (transformed and/or corrected for coverage) values used for Genome Wide Association Studies (GWAS). (2) GWAS results (filtered for -log(p)>1) for all processed average methylation values are available with the .gwas extention and can be easily opened with Integrative Genomics Viewer (https://software.broadinstitute.org/software/igv/), using the reference genome published by Nunn et al. 2021 (https://pubmed.ncbi.nlm.nih.gov/34990041/). (3) Variance Decomposition Analysis results of Differentially Methylated regions called using scripts available at https://github.com/Dario-Galanti/popDMRs_refine_VCA.