Monday: DNA methylation analysis with short reads (Illumina WGBS and EM-Seq) – 2-7pm Berlin time
- Presentation: Origin and evolution of DNA methylation in eukaryotes: from parasite defence to gene regulation.
- Presentation: Introduction to short-read format and processing (WGBS/EM-Seq).
- Lab 1: Short-read processing:
o QC, filtering, trimming
o Genome preparation
o Alignment, deduplication
Tuesday: DNA methylation analysis with short reads (Illumina WGBS and EM-Seq) – 2-7pm Berlin time
- Presentation: Introduction to DNAm in plants.
- Presentation: Population epigenomics: patterns and drivers of DNAm variation in natural populations.
- Lab 2: Short-read processing:
o Conversion efficiencies (lambda/pUC19)
o Methylation count files
o Accounting for SNPs
Wednesday: DNA methylation analysis with long reads (Oxford Nanopore) – 2-7pm Berlin time
- Presentation: Nuances of DNA methylation data: sex, tissue, age, imprinting and allelic-variation.
- Presentation: Introduction to long-read format and processing (Nanopore/PacBio).
- Lab 3: Nanopore long-read processing:
o Fast5/pod5 generation, Pod5 tools
o Dorado/Guppy, and models
o Modbam2bed/Modkit
o Example: methylation haplophasing
Thursday: Identification of differentially methylated sites and regions and integration with SNP data – 2-7pm Berlin time
- Presentation: DNAm and genetic variation: biological insights and analytical hazards.
- Presentation: Introduction to differential DNA methylation.
- Lab 4: Differential DNA methylation:
o Testing for differentially methylated sites and regions between populations and conditions
o Visualising differential methylation
o Accounting for SNPs
Friday: Integration of DNA methylation and gene expression and open session on your own data / experiments – 2-7pm Berlin time
- Lab 5: Integration of DNA methylation and gene expression:
o Quantifying genes/exon/intron levels
o Correlational plots
o Overlap of differential methylation and differential expression
- Open session: Group questions / discussion:
o Follow up on any course material
o Student questions on their own data / experimental plans