Spatial gene expression at species agnostic level

Spatial gene expression at species agnostic level is organized by European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL - EBI) and will be held from Mar 02 - 06, 2026 at EMBL Advanced Training Centre (ATC), Heidelberg, Baden-Wurttemberg, Germany.

Course overview:
This interactive course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. Objectives The Visium Cytassist Spatial Gene Expression Solution uses probes targeting the whole transcriptome for intact tissue sections in morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Cytassist Spatial Gene Expression slides. Through practical work in the lab and theoretical sessions, the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training in spatial transcriptomics data analysis.

Modules/resources:

• Overview of 10x Genomics Visium Cytassist Spatial Gene Expression technology
• Focusing on fresh-frozen samples with Hematoxylin and Eosin (H&E) staining
• Alternative staining by immunofluorescence and usage of FFPE samples as starting material
• Pre-recorded application lectures on spatial transcriptomics
• Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
• Visium Spatial Gene Expression data analysis using Loupe Browser (license-free)
• 1-on-1 project consultation with application specialist (optional service offered at the discretion of the individual participant)

Learning outcomes:
After this course you will be able to:

• Appreciate the importance of spatially resolved transcriptomics data
• Realise the significance of properly prepared tissue sections by cryosectioning
• Understand the requirements for brightfield and fluorescent tissue slide imaging
• Analyse and interpret data output using Loupe Browser