Monday - DNA methylation analyses with short reads (Illumina BS-seq) - 2-8 pm Berlin time

Lecture 1
•    DNA methylation in the field of Ecology and Evolution: what are the patterns of diversity of DNA methylation between species, across populations and within the genome?
•    WGBS and RRBS protocols and sequence format. General processing of bisulfite data with a reference genome

Lab 1 (Part 1)
•    Introduction to files (header etc)
•    Quality Check (QC)
•    Genome prep, alignment and methylation calling, mbias using RRBS data (reference genome, Bismark)

Tuesday: Second part of short read Lab + Lectures on DNA methylation analyses with long reads (PacBio and Oxford Nanopore) - 2-8 pm Berlin time

Lecture 2
•    DNA methylation in an ecological and evolutionary context
•    DNA methylation regulation in plants and animals.

Lab 1 (Part 2)
•    QC, read filtering and trimming using WGBS data
•    alignment, deduplication, methylation calling using WGBS data (ref. genome, Bismark)
•    Estimation of the non-conversion rate (bisulfite conversion efficiency)
•    Inference of individual cytosine methylation from read counts (binomial test on individual cytosines controlling for non-conversion rates for Illumina, binomial test on genes compared to genome average) + metaplots (Short R lab)

Wednesday: Lab on long read analysis + Statistical inferences on DNA methylation data - 2-8 pm Berlin time

Lecture 3
•    DNA methylation, gene expression and epigenomic conflicts
•    Tissue-specific differences in DNA methylation. What tissue to use and why it matters
•    Sex-specific differences in epigenetic marks, sex chromosomes and sex determination
•    PacBio and Ofxord Nanopore protocols and sequence formats. General processing of data.

Lab 2
•    Processing of long-read data for DNA methylation inference using ONT data (diploid and haplotype-specific inferences)
•    PacBio DNA methylation inferences

Thursday: LAB on selection detection on DNA methylation + the importance of DNA methylation in Ecology and Evolution - 2-8 pm Berlin time

Lecture 4
•    Inference of differentially methylated sites (DMS) and regions (DMR)
•    Inferences of epigenetic differences in presence of genetic variation (pedigrees or structured sample)

Lab 3
•    Clustering and visualization of samples
•    strand specificity option
•    Statistical epigenetics –  use of methyKit and mixed models for inferring differentially methylated sites and regions between groups
•    Mixed models in R to call differential methylation while controlling for genetic variation
•    Validation plots (overdispersion)

Friday: DNA methylation and gene expression - 2-8 pm Berlin time

Lecture 5
•    Strand specific DNA methylation and parental imprinting in plants
•    Recapitulation of DNA methylation analyses in Ecology and Evolution

Lab 4
•    Methods to infer selection acting on DNA methylation (Site Frequency Spectrum)
•    DNA methylation and its link to gene expression (plots and statistics in R)
•    Follow-up on LAB 3 on differential DNA methylation
•    Student questions & feedback