The structure and clarity of 10X genomics’ own User Guide is excellent and we highly suggest you simply download and follow along with the latest version of their protocol here. This is the protocol for single-plexed samples. This is an option for multiplexing up to 4 times as many samples. We encourage you to start with single-plexed samples before proceeding to multiplexed samples.
We have both a Chromium Controller and a Chromium X. The Chromium X can do all that the Chromium Controller can do, as well as all the newer assays. Unless otherwise necessary, use the Chromium X.
Fixed Tissue and Tissue Dissociation
It is important that you follow 10X protocol for fixing and dissociating your tissue. The protocol for fixing and dissociating tissue is here. The protocol for fixing sample that has already been dissociated is here.