Course Single Cell and Spatial OMICS – Basic Course (module 1)

The course Single Cell and Spatial OMICS – Basic Course (module 1) is being offered by the Graduate School of Health, Aarhus University, 2024.

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: 
The analyses of DNA mutation and gene expression (from DNA to protein level) in tissues and organs have moved from bulk into single cell and spatially resolved resolutions. Technologies enabling high throughput single-cell and spatial genomic, transcriptomic, and proteomic (OMICS) analyses have been rapidly developed over the last few years. Most importantly, these technologies have become important methods for modern research in life sciences, biology, and medicine. There is therefore a need to systematically introduce PhD students to the underlying principles of the different single cell sequencing technologies, spatial RNA and protein profiling technologies. This includes understanding of the platforms developed for high throughput single cell and spatial OMICS analyses, their potential applications, advantages and limitations, and importantly how to analyze and understand the vast amount of data generated by these methods. The aim of this PhD course is to introduce students the principles, developments, and applications of the single cell and spatial OMICS technologies, which can be used to study genomics, transcriptomics, and proteomics at single-cell and spatially resolved resolutions. Technologies, such as single cell DNA sequencing, single cell RNA sequencing, single cell proteomics profiling, spatial RNA sequencing, spatial protein profiling, will be introduced by this course. Most importantly, this PhD course aims to prepare students with knowledge and training on how to process, analyze, interpret, and critically evaluate single cell and spatial OMICS data. The course will be organized in collaboration with the national roadmap center CellX. 

The Basic Course (module 1) will be focusing on introducing the theory, technology, and applications of various up-to-date single cell and spatial OMICS technologies. Basic introduction of data generation and preliminary data analysis will be provided in the basic course.

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.
7. Critically read and evaluate studies within the field of single cell and spatial sequencing.

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

Content: The course covers:

• Single cell RNA sequencing
• Spatial transcriptomics
• Single cell proteomics
• Spatial proteomics (including metabolism)
• Single cell DNA sequencing
• Single and Spatial imaging
• Introduction to R and Python
• Introduction to data analysis pipelines
• Galaxy / Single Cell Omics
• CellX
• Applications highlights, including (but not limited to) neurosciences, organogenesis, cancers

Instructors: 

Per Qvist per.q@biomed.au.dk

Yonglun Luo alun@biomed.au.dk

Jonathan Brewer brewer@memphys.sdu.dk

Konstantin Khodosevich konstantin.khodosevich@bric.ku.dk

Kasper Thorsen kasper.thorsen@clin.au.dk

Juan Luis Garcia Rodriguez juanlgr@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 (other)

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:

• 13 May 2024 09:00 - 16:00
• 14 May 2024 09:00 - 16:00
• 15 May 2024 09:00 - 16:00
• 16 May 2024 09:00 - 16:00
• 17 May 2024 09:00 - 16:00