Missing Fixation and Permeabilization Controls

Symptom

Difficulty interpreting results due to unknown effects of fixation and permeabilization on fluorescence intensity and population distribution. Unable to distinguish artifacts from true biological changes.

1. 1 Failure to include unfixed controls to assess fixation-induced fluorescence changes
2. 2 No comparison between different permeabilization methods
3. 3 Lack of isotype or negative controls processed with same fixation protocol
4. 4 Incomplete validation of fixation/permeabilization effects on specific fluorophores

1. 1 Include controls for fixation/permeabilization effects in every experiment
2. 2 Run parallel samples with and without fixation to assess fluorescence shifts
3. 3 Test multiple permeabilization conditions with appropriate controls
4. 4 Document fixation/permeabilization impact on each fluorophore in the panel

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