Data from : ‘Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar’.

Details

11 ADDITIONAL FILES Additional file 1. CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (metadata). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the Gene Expression Omnibus (GEO) database (submission GSE225596). Additional file 2. CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (processed data). Additional file 3. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Additional file 4. POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1, E. SPC1 versus UKD2 Additional file 5. CSV-file with the raw data of the bud set observations in the common garden experiment (raw data). Additional file 6. HTML-file with the R source codes to reproduce the results of the bud set analysis (code, R script). Additional file 7. A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (code, Snakefile). Additional file 8. RMD-file with the code to reproduce the analyses to identify differential methylated predefined regions (code, R script). Additional file 9. R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (code, R script). Supporting files 1. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (processed data). Supporting files 2. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (processed data).

Uitgeverij	zenodo
Geografische dekking	Europe

Teams

• Genetische Diversiteit
• Biometrie, methodologie en kwaliteitszorg

INBO Onderzoeksdomein(en)

• Bos

Taxonomische lijst

• populier (Populus spp.)

Beleidsmatig

• milieubeleid

EWI Biomedische wetenschappen

• B003-ecologie