10x Genomics workflows require compatible thermal cyclers to be programmed to execute various steps. This Technical Note provides guidance for downloading protocols that can be used to program BioRad C1000 and Eppendorf Mastercycler X50s thermal cyclers. Before running a downloaded protocol, refer to the most current version of the product-specific User Guide to confirm the protocol steps and to modify the number of cycles or incubation time as required. Cycle number and incubation time may require adjustment depending on library, cell or tissue type, cell loading, and/or input mass. Edit and save the updated protocol with a new name to prevent confusion.