Is it okay to stain cells for both intercellular and surface markers for FACS analysis?

Yes, it is possible to perform both intracellular and surface staining on the same cells; however, they should not be done in the same step. This is because the fixation and permeabilization that is necessary for intracellular staining may decrease the signal of surface antigens. Therefore, it is best to perform surface staining first before fixing and permeabilizing the cell for intracellular staining.