10x Genomics Single Cell protocols require a suspension of viable single cells or nuclei as input. Minimizing the presence of cellular aggregates, dead cells, noncellular nucleic acids, and potential biochemical inhibitors of reverse transcription is critical to obtaining high-quality data. This Cell Preparation Handbook describes best practices to help maintain cell viability and maximize sample quality during sample preparation. General protocols for sample handling, purifying, and counting for both abundant and limited cell suspensions are also provided here. The general protocols described here are expected to be compatible with many, but not all cell and sample types. Additional optimization may be required for sensitive samples and solid tissues. For additional information on preparation of specific sample types, consult the Demonstrated Protocols available on the 10x Genomics Support website.