Preparation of the Cytoflex SRT for Fluorescence-Activated Cell Sorting (FACS) of Microbes and Submicron (Small Particle) Samples such as Virus-like Particles (VLPs), Extracellular Vesicles, and more v1

This protocol is specific to the Beckman Coulter Cytoflex SRT cell sorter to prevent long-term contamination and disrupt potential formation of unwanted biofilms following the sorting of microbial samples and/or to clean the flow cell and system in preparation for running submicron (small particle) samples. This is suitable for submicron/small particle sample types including, but not limited to microbes, virus-like particles (VLPs), extracellular vesicles, organelles, and more. Instructions are included to prepare the instrument for running samples that will require DNA-free preparation for whole genome amplification prior to genomic sequencing. Decontamination protocols for cell sorters and cytometers are instrument specific; while best practices always apply, protocols for one instrument make/model must be thoughtfully adapted for other instruments. This protocol is suitable for use in Shared Resource Laboratory (SRL) settings as well as individual research labs. This is a protocol that accompanies the following article: Tijerina, J.C., Martinez-Hernandez, F., Beilinson, V., Finney, O., Orphan, V.J., & Diamond, R. A. (2025). Preparation of cuvette-based sorters for sorting submicron microbial cells and viruses from environmental and biological samples. Current Protocols, 5, e70176.doi: 10.1002/cpz1.70176 .Additional necessary background and associated protocols are found in that protocol article.