Single Cell RNA

Course Description

Single-cell sequencing is revolutionizing our understanding of essential biological processes, including development, immunity, and pathology. Contemporary techniques empower us to delineate gene expression, cell surface proteins, TCR/BCR receptors, and chromatin accessibility profiles of thousands of cells at remarkable resolution, facilitating comprehensive characterization of diverse cell populations, such as tumors or entire organisms.

As a state-of-the-art research and training facility, jointly operated by ETH and the University of Zurich, the Functional Genomics Center Zurich (FGCZ) offers a five-day hands-on course to help participants master rapidly developing single-cell transcriptomic techniques. The practical component includes library preparation on the 10x Genomics platform using live single-cell suspensions, with the library prep following the kit manual.
Sequencing will be conducted on a benchtop sequencer, and participants will receive an introduction to the analysis of the resulting data along with exercises.

The lectures will cover single-cell and multiomic technologies, their applications, and data analysis principles. An entire module has been added for single-cell transcriptomics, encompassing both experimental techniques and data analysis.

Course Programme

Transcriptomics

• Introduction to next generation sequencing and available technologies
• Overview of single-cell sequencing methods
• Introduction to spatial transcriptomics technologies

Single-Cell Library Preparation and Sequencing

• Loading and running a 10x Genomics chips with live cells to produce cDNA
• Using the cDNA to prepare a library ready for Illumina sequencing
• Quality control of sequencing libraries
• Sequencing libraries on a NextSeq 2000

Data Analysis

• Run QC: Criteria for run performance
• Read QC: Metrics for evaluating read quality
• Running CellRanger for initial analysis of single-cell data
• Quality control and filtering: Identifying low-quality cells, doublets, and ambient RNA contamination
• Data preprocessing with Seurat: Normalization, feature selection, and scaling
• Dimensionality reduction: PCA and UMAP visualization
• Cell clustering and identification of immune cell populations
• Marker gene detection and cell type annotation of PBMCs
• Differential expression analysis between clusters
• Visualization best practices for single-cell data interpretation

Learning outcomes

By the end of this course, participants  will be able to:

1. Summarize the principles of current single-cell sequencing technologies 
2. Design an appropriate scRNA-seq workflow to apply to their own research project
3. Perform a 10x Genomics library preparation and sequencing procedures in the laboratory
4. Apply basic bioinformatics tools for the processing and analysis of single-cell datasets
5. Critically evaluate sequencing and analysis results

Please note, that the above prices can only be applied if the tuition fee is paid through an internal, i.e. University of Zurich or ETHZ, account (valid Kostenstelle/PSP-Element).

An invoice will be issued upon registration. Registered participants will receive an email containing an “Application Form”, which must be signed by their respective supervisor.

The signed form should then be returned to the FGCZ via email as a PDF. Only upon receipt of the signed “Application Form”, will the participant’s registration be considered complete, and their place in the course officially confirmed.

Cancellation Policy

Please note that, due to the high demand for this course, any change related to your participation must be communicated as soon as possible, but not later than twenty (20) working days prior to the course start date. The notice must be sent via email to . If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.