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