Biological systems are made of mixtures of heterogeneous cell populations that are difficult to characterize using conventional bulk methods. Today, a deeper understanding of biological systems requires applying state-of-the-art genomics methods with single-cell resolution. Indeed, single-cell genomics technologies provide a high-resolution and comprehensive view of the transcriptome of the different cellular constituents of tissues, organs, and even whole organisms under different states or conditions, pushing the frontiers in our understanding of normal physiology and disease. In recent years, several platforms for unbiased single-cell analysis have been developed. Amongst them 10x Genomics, the current leading commercial solution for high throughput single-cell RNA-seq analysis, makes this technology available to researchers in the academy, hospitals and industry. Yet, single cell analysis requires proper understanding of its capabilities and limitations.
The course will be composed of a comprehensive introduction to the field, a hands-on session, single cell data analysis, and a single cell genomics interpretation. You will be introduced to single-cell genomics technologies and learn conceptual tools for understanding and designing single-cell based experiments, with an emphasis on single cell gene expression profiling. This will include hands-on practice of the 10x Genomics technology and interpretation of the data generated. In addition, other single-cell genomics tools will also be covered, such as multiomics solutions, including analysis of surface protein expression and gene expression in the same single cell, chromatin accessibility at the single-cell level (single cell ATAC-seq), CRISPR-based gene perturbation with single-cell resolution and spatial transcriptomics analysis. Examples of applications of these technologies will be discussed in a seminar format.