This analysis contained the identification of DNA methylation sites in the context of CpG islands and differentially methylated regions (DMRs) with MethylScore. Further the mRNA sequencing data were analyzed to differentially expressed genes. Differentially expressed genes and identified DMRs were correlated. Finally DMRs and their expression changes were characterized in their genomic context. All raw sequencing data used as input for analyses to obtain the data in this repository are deposited in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA1163668 (http://www.ncbi.nlm.nih.gov/bioproject/1163668). The genome assembly and annotation data used here were obtained from DataverseNO (https://doi.org/10.18710/GXMSUH). This genome assembly is based on the raw sequencing data deposited under BioProject ID PRJNA1119394 (http://www.ncbi.nlm.nih.gov/bioproject/1119394). Together these data were used to identify CpG sites genome wide and further identify differentially methylated regions. The corresponding mRNA was utilized to identify transcriptional changes and enable a comparison of differentially methylated genes with differentially expressed genes. Scripts are available in the GitHub repository WholeGenomeBisulphiteSequencing (https://github.com/MagdalenaWinklhofer/WholeGenomeBisulphiteSequencing.git).

FASTQC, 0.11.9

TrimGalore, 0.6.10

BWA-METH, 0.2.7

MethylScore, 0.2

SAMtools, 1.17

Subread, 2.0.3

DESeq2, 1.40.2

goseq, 1.52