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Autofluorescence is the inherent fluorescence of compounds present in cells. These include compounds such as NAD(P)H, Collagen, and Tryptophan. Autofluorescence can negatively impact the sensitivity of flow cytometry measurements, especially in large cells... (Read more below.)
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Autofluorescence increases as the size of the cell increases, which can impact the background signal. It can also impact compensation, especially if the control positive and control negative have different autofluorescent signals, which will result in incorrect compensation.
Not everything about autofluorescence is bad, as some subcellular populations can be identified based on the autofluorescent signal. A perfect example of this is identification of alveolar dendritic cells as compared to alveolar macrophages.
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