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Isotype controls have been optimized for cell surface staining to control for non-specific binding of antibody and fluorophore. They are therefore only one of several controls that may be performed to accurately detect your positive population. Because intracellular staining requires fixation and permeabilization which can affect antigen detection, autofluorescence, fluorophore brightness and cell morphology, other controls are necessary. These can include biological controls, such as stimulation/blocking experiments and negative/positive controls, which are described in more detail below.
To find out more about optimizing your intracellular staining go to our intracellular staining tips page or download our handy PDF.