Single-cell genomic technologies have matured and are now widely employed to gain novel insights in multiple areas of biological research. Given the level of interest in these methods, one limiting factor to their broader dissemination is the availability of high-quality, step-by-step methods on the best techniques to prepare tissues and cellular samples for single-cell library generation. 

The dominant platform in this arena is the 10X Chromium Controller. 10X Genomics offers standardized kits and reagents for Gel Beads-in-Emulsion (GEM) generation and accompanying protocols for sample preparation. Still, laboratories new to these techniques may experience a learning curve when preparing unique biological samples into single-cell or single nuclei suspensions for GEM isolation. The research community would immensely benefit from the widespread sharing of the expertise developed by early adopters of these techniques. This series of articles seeks to fill this need. 

Through this Methods Collection, JoVE will provide a set of methods and short accompanying videos to share subtle optimization tricks and best practices for single-cell sample preparation and analysis. These methods, which leverage the detailed knowledge of current users of this technology in a peer-reviewed format, will assist other laboratories in applying single-cell RNA, ATAC, surface receptor, and multiomic analyses to novel research fields