Educators:
Fabian Müller
Jörn Walter (HD-HuB)
Saarbrücken de.NBI team (HD-HuB)

Date:
July 29 – August 12

Location:
Universität des Saarlandes

Outline:
This workshop offers an introduction into bioinformatics methods and tools for integrated NGS-based (NGS = next-generation sequencing) epigenome analysis. The course starts with two lecturing days introducing/refreshing participants' knowledge of epigenetic gene regulation and introduces a series of experimental methods to profile the epigenome. You will then delve into the theoretical background of bioinformatics methods and software tools used for data processing. You learn about quality control methods, exploratory analyses, differential analyses, and integration of multiple data modalities. Four epigenomic data modalities will be analysed in detail: gene expression, DNA methylation, chromatin accessibility, and histone modifications. The theoretical knowledge conveyed in the lectures will then be solidified in a four day hands-on workshop, in which the participants in groups of 2 will employ the introduced methods.

Participants should be familiar and trained in the use of UNIX shell and R. To make them familiar with the working environment all participants are obliged to successfully participate in a Data Camp tutorial provided before the course starts.

Content:
Precourse work:
- Exercises in UNIX shell and R usage via a DataCamp module.
Lectures followed by practical exercises:
- Introduction into principles of epigenetic gene regulation.
- Experimental techniques and bioinformatic analysis for gene expression (RNA-seq).
- Experimental techniques and bioinformatic analysis for DNA methylation (WGBS/Bisulfiteseq, microarrays, enrichment-based methods, etc.).
- Experimental techniques and bioinformatic analysis for chromatin accessibility (ATAC-seq, DNase-seq, NOMe-seq, etc.).
- Experimental techniques and bioinformatic analysis for histone modifications (ChIP-seq, CUT&RUN, etc.).
- Integrative data analysis: Dimension reduction, clustering, differential analysis, segmentation, imputation.
- Emerging epigenome profiling technologies (including single-cell and multiome methods).

Schedule
- April 29 to July 28 (self-guided): (Re-)Familiarize yourselves with the UNIX shell and R programming in the DataCamp classroom and complete the mandatory courses - Online.
- July 29 to 31: Six theoretical lectures (90 minutes each) introducing the biological and bioinformatics background (Can be attended online).
- August 5 -9 (9am – 5pm): Hands-on workshop (in presence).
- August 12: Presentation of results. (Mandatory for participants who aim to obtain full credit points for the course. (in presence)

Admission:
To enroll, participants should have a basic knowledge of modern genomics and epigenetics. Basic skills for script-based programming using the R language and the use of UNIX is mandatory. Participants will have the opportunity to (re-)familiarize themselves using a DataCamp classroom provided upon registration. In this DataCamp mandatory courses on UNIX shell usage and R scripting will have to be completed in the DataCamp classroom before the lecture of the workshop starts (i.e., by July 28, 2024). The course will be limited to up to 10 external participants. Non-bioinformatics participants will be accepted on an individual basis if they can demonstrate that the bioinformatic requirements are met. Certificate(s) To obtain a certificate of participation participants have to: 1. Successfully participate in the introductory course on DataCamp. 2. Fully attend all lectures (online) and the course (in person) To obtain a qualified certificate of participation (5 Credit Points) participants need to: 1. Complete the introductory course on DataCamp. 2. Pass the test on lectures. 3. Hand in a notebook-based (R Markdown) protocol. 4. Give a final presentation (n person).

Learning Goals:
- Understand the bioinformatics processing of DNA methylation, histone modifications, gene expression, and chromatin accessibility.
- Prepare and describe raw read files.
- Evaluate NGS data.
- Understand the individual role of each assay-specific data.
- Learn how to integrate various modalities and how to decipher the cross-talk between various epigenomic modifications.

Prerequisites:
The course requires basic skills in:
- Linux/bash
- R

Keywords:
DNA methylation, histone modifications, RNA-Seq, ATAC-Seq, integrative analysis, dimension reduction, clustering, differential analysis, segmentation, imputation.

Tools:
nf-core, conda, singularity, RnBeads, methylSeekR, chromHMM, ChrAccR, edgeR, deeptools.