Educators:
Nihit Aggarwal, Dr. Gilles Gasparoni, Dr. Thomas Hentrich, Prof. Dr. Jörn Walter, (HD HuB)

Date:
December 5th and 6th, 2024.

Location:
Saarbrücken

Contents:
The workshop aims to convey basic knowledge on the bioinformatic processing of DNA methylation data. We will explore the important role of DNA methylation and examine various methodologies for its measurement, particularly emphasizing methylation arrays. Participants will learn on how to access methylation data from online platforms and set up their analysis environment utilizing RStudio and RnBeads. The course will guide through the entire process of handling array-based methylation data, starting from the initial import to conducting thorough quality assessments, and achieving standardization. We will generate comprehensive methylation profiles and engage in both exploratory and comparative studies to detect methylation differences across various biological sites, cellular compositions, and pathological conditions (Neurodegenerative disease). The workshop will also touch advanced topics such as deconvolution methods to discern cell type and disease-specific methylation distinctions. Additionally, participants will acquire the skills to apply these methodologies to their own array data after the workshop.

Learning goals:
- Importance and relevance of DNA methylation
- Introduction to various technologies for DNA methylation measurement, with a focus on methylation arrays - Retrieving array based methylation data.
- Preparation of environment (Rstudio and RnBeads)
- Processing of array based data
- data import
- quality check
- normalization
- generating methylation matrix
- Performing exploratory analysis with ggplot
- Differential analysis
- sites/regions
- cell types
- disease
- Understanding cell type and disease specific differences
- Reference-based deconvolution

Prerequisites:
- The course requires basic skills in R.
- Laptop with at least 4GB RAM. (More information about the packages needed will be provided in due time)

Keywords:
DNA methylation, Methylation array, RnBeads, Neurodegenerative disease, Deconvolution Tools: R, Rstudio, RnBeads