Immunophenotyping challenging tissue types using high-dimensional full spectrum flow cytometry

Technological advancements in fluorescence flow cytometry and an ever-expanding understanding of the complexity of the immune system, have led to the development of large flow cytometry panels, reaching up to 40 markers at the single-cell level. Full spectrum flow cytometry, that measures the full emission range of all the fluorophores present in the panel instead of only the emission peaks is now routinely used in many laboratories internationally, and the demand for this technology is rapidly increasing. With the capacity to use larger and more complex staining panels, optimized protocols are required for the best panel design, panel validation and high-dimensional data analysis outcomes. In addition, for ex vivo experiments, tissue preparation methods for single-cell analysis should also be optimized to ensure that samples are of the highest quality and are truly representative of tissues in situ. Here we provide optimized step-by-step protocols for full spectrum flow cytometry panel design, tissue digestion and panel optimization to facilitate the analysis of challenging tissue types.