Case–control Xenium: from cells to biology
Training materials for the 2026 V4SDB Student Summer School
Instructors:
Katarina Dragicevic (BRIC University of Copenhagen)
katarina.dragicevic@bric.ku.dk
Dorottya Ralbovszki (BRIC University of Copenhagen)
dorottya.ralbovszki@bric.ku.dk
Workshop Overview
Xenium spatial transcriptomics measures targeted gene expression at single-cell resolution while preserving the physical organization of the tissue. This makes it possible to study which cell populations are present, what genes they express, and where they are located. In case–control human brain data, however, the challenge is not simply to generate clusters: cell identities must be supported by marker genes and reference data, and disease comparisons must respect the donor as the biological replicate.
In this workshop, participants will analyze Xenium data from the human dorsolateral prefrontal cortex, comparing schizophrenia and neurotypical control donors. Working in R and Google Colab with Seurat, participants will start from a prepared object after quality control, normalization, and scaling. They will move step by step through dimensionality reduction, clustering, marker-based cell-type annotation, comparison with a published human DLPFC single-nucleus reference, visualization of annotated cells in tissue space, donor-level cell-type composition, and cell-type-specific pseudobulk differential expression.
By the end of the workshop, participants will be able to explore a single-cell spatial object, cluster cells and interpret a UMAP, annotate broad brain cell types using multiple sources of evidence, map annotations back into tissue space, compare cell-type proportions between groups, and perform donor-aware differential expression. Throughout the analysis, emphasis is placed on avoiding pseudoreplication, recognizing the limitations of a targeted 300-gene panel, and separating exploratory teaching results from publication-level biological conclusions.
Notebook
Click here to access the notebook.