This workshop is an introduction to differential gene expression analysis of medium-sized single-cell RNA-seq (scRNA-seq) obtained using the 10x Genomics Chromium System. Participants will learn about the basic concepts behind the technology, its applications and concepts, and go through a hands-on exercise where they will perform a re-analysis of a sample of ~3,000 cells from the Mouse Cell Atlas (MCA). For this they will make use of a user-friendly web application built on top of the popular Seurat package, that allows interactive exploration of the concepts involved in the analysis, including filtering, normalization, dimensionality reduction, clustering, and marker gene identification.

• Single-cell RNA-seq (scRNA-seq) versus (bulk) RNA-seq.
• Understanding the scRNA-seq UMI count matrix.
• Overview of scRNA-seq data analysis and basic concepts.

• Quality control and filtering.
• Normalization
• Dimensionality reduction (PCA, t-SNE, UMAP).
• Clustering of cell subpopulations.
• Marker gene identification and differential expression analysis.