Course Introduction to Single-Cell and Spatial OMICS: Principles, Technologies, and Basic Data Analysis

The course Introduction to Single-Cell and Spatial OMICS: Principles, Technologies, and Basic Data Analysis is being offered by the Graduate School of Health, Aarhus University, 2025.

Criteria for participation: 
University degree in medicine, dentistry, nursing, or Master’s degree in other fields and/or postgraduate research fellows (PhD students and research-year medical students).

Aim: 
Advancements in genomic, transcriptomic, and proteomic analyses have revolutionized our understanding of biological systems by enabling single-cell and spatially resolved investigations. These high-throughput technologies have rapidly evolved, transitioning from bulk analyses to single-cell and spatial resolutions, providing unprecedented insights into tissue heterogeneity, cellular interactions, and molecular mechanisms in life sciences, biology, and medicine.

This PhD course aims to provide a comprehensive introduction to the principles, developments, and applications of single-cell and spatial OMICS technologies. Students will gain fundamental knowledge of sequencing and profiling methods used to study genomics, epigenomics, transcriptomics, metabolomics, and proteomics at both single-cell and spatially resolved levels. The course will cover key technologies, including:

• Single-cell OMICS: Single-cell DNA sequencing, single-cell RNA sequencing, and single-cell proteomics profiling
• Spatial OMICS: Spatial RNA sequencing, spatial protein profiling, and spatial metabolomics profiling

In addition to understanding the principles, advantages, and limitations of these platforms, students will be introduced to data generation, processing, and preliminary analysis of single-cell and spatial OMICS datasets. Emphasis will be placed on developing the ability to critically evaluate and interpret complex multi-omics data.

This course will be organized in collaboration with the national roadmap center CellX and will include theoretical lectures, discussions on technological advancements, and practical insights into data analysis. The course is designed to equip PhD students with the foundational knowledge and analytical skills necessary for applying single-cell and spatial OMICS in their own research.

Learning outcomes: By the end of the course, students are expected to:

1. Articulate and demonstrate systematic knowledge of single cell and spatial OMICS.
2. Interpret and communicate new results within the field.
3. Describe and critically evaluate data generated with single cell and spatial OMICS methodologies.
4. Independently and properly select the right single cell and spatial OMICS technologies for specific research questions.
5. Understand the basic pipelines and tools needed for single cell and spatial OMICS analysis.
6. Understand the individual steps of the analysis pipeline for single cell RNA sequencing data.

Workload: The full workload of the course is expected to be 55 hours

Content: 
The course covers:

 Single-cell RNA sequencing (scRNA-seq) – Principles, platforms, and applications in biological research.

Single-cell ATAC sequencing (scATAC-seq) – Chromatin accessibility profiling at single-cell resolution.

Spatial transcriptomics – Technologies for spatially resolved gene expression analysis.

Single-cell proteomics – Methods for protein profiling at single-cell resolution.

Spatial proteomics – Techniques for mapping protein distributions within tissues.

Spatial metabolomics – Profiling and visualization of metabolite distributions in tissues.

Single-cell and spatial imaging – High-resolution imaging approaches for cellular and molecular visualization.

Introduction to data analysis pipelines – Overview of computational workflows for processing and analyzing single-cell and spatial OMICS data.

Galaxy for Single-Cell OMICS – Utilizing the Galaxy platform for data analysis and workflow automation.

CellX – Overview of the national roadmap center and its role in advancing single-cell and spatial OMICS research.

Application highlights – Case studies and real-world applications in fields such as neuroscience, organogenesis, and cancer research.

Instructors: 

Kyung Min Noh noh@embl.de

Ian Geoffrey Mills ian.mills@biomed.au.dk

Per Qvist per.q@biomed.au.dk

Yonglun Luo alun@biomed.au.dk

Jonathan Brewer brewer@memphys.sdu.dk

Kasper Thorsen kasper.thorsen@clin.au.dk

Lasse Sommer Kristensen lasse@biomed.au.dk

Ermelinda Porpiglia eporpiglia@biomed.au.dk

Lei Cheng lche@biomed.au.dk

Alexander Schmitz alex.schmitz@biomed.au.dk

Ebbe Norskov Bak ebbebak@clin.au.dk

Venue: Aarhus University, Aarhus

Participation in the course is without cost for:

• PhD students, Health Research Year students from Aarhus University
• PhD students enrolled at partner universities of the Nordoc collaboration
• PhD students from other institutions in the open market agreement for PhD courses

Course dates:

• 23 June 2025 09:00 - 16:00
• 24 June 2025 09:00 - 16:00
• 25 June 2025 09:00 - 16:00
• 26 June 2025 09:00 - 16:00
• 27 June 2025 09:00 - 16:00