de.NBI-Workshop: DNA Methylation: Design to Discovery

Workshop page

Course website

Location: Saarbrücken and online (hybrid)

Overview

This workshop aims to convey fundamental knowledge on the bioinformatic processing of DNA methylation data. We will explore the biological relevance of DNA methylation and review major methodologies for its measurement, with a particular focus on methylation arrays.

Participants will learn how to access publicly available methylation datasets and how to set up a reproducible analysis environment using RStudio and RnBeads. The course covers the complete workflow for array-based DNA methylation analysis, from data import to quality control, normalization, and downstream analysis.

Comprehensive methylation profiles will be generated, followed by exploratory and comparative analyses to identify methylation differences across biological sites, cell types, and pathological conditions, with a focus on neurodegenerative diseases. Advanced topics such as reference-based deconvolution will be introduced to disentangle cell-type- and disease-specific methylation signals.

Participants will also gain the skills needed to apply these methods to their own array-based methylation data after the workshop.

Learning Goals

• Understand the importance and biological relevance of DNA methylation
• Overview of DNA methylation measurement technologies, with emphasis on methylation arrays
• Retrieval of array-based methylation data from online repositories
• Preparation of the analysis environment (RStudio and RnBeads)
• Processing of array-based methylation data:
  • Data import
  • Quality control
  • Normalization
  • Generation of methylation matrices
• Exploratory data analysis using ggplot2
• Differential methylation analysis:
  • Sites and regions
  • Cell types
  • Disease-specific effects
• Understanding cell-type- and disease-specific methylation differences
• Reference-based deconvolution approaches

Prerequisites

• Basic knowledge of R programming
• Laptop with at least 4 GB RAM
• Additional information on required packages will be provided in advance
• Data
  • You can download the data before hand from here

Tools and Keywords

Keywords: DNA methylation, methylation arrays, RnBeads, neurodegenerative disease, deconvolution
Tools: R, RStudio, RnBeads

Contact

Nihit Aggarwal
Email: nihit.aggarwal@uni-saarland.de

Registration

Interested participants can register by sending an email to nihit.aggarwal@uni-saarland.de with the following information:

• Name
• E-mail
• Specialization / background
• University / institute