I would like to do next generation sequencing on cells sorted based on an intracellular stain. Is there a best practice for how to fix the cells such that my sequencing run is not compromise?
There are kits around which allow DNA/RNA isolation from fixed samples, but they are by default less efficient that the ones, which work with unfixed material. So the main suggestion is NOT to fix your cells prior NGS. The conventional way is to spin your cells after FACS and freeze the pellet in LN (with storage at -80). Then you can isolate DNA/RNA from you frozen pellet and use as input for NGS kits.