In addition to staining and isotype controls, you should also consider biological controls that will enable you to determine staining specificity and experimental limitations. They are important for all staining, but are more important for intracellular staining which can have higher background fluorescence. Controls include known negative samples and known positive samples.
Examples of these are:
For some experiments such as cytokine release measurement, an unstimulated and fully stimulated sample is important to determine both positive results and the dynamic range of fluorescence staining.
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