Dear all, I am trying to compare cell surface expression of TCR/CD3 structures on naive versus activated T lymphocytes. I have a question related to the interpretation of the data. What if two cell types express similar levels of a given protein (as judged by the mean channel fluorescence following staining with a directly labeled antibody), but display different autofluorescence ? My guess is that since autofluorescence is at least an order of magnitude lower than the Ab-FITC signal, just ignore it and conclude that both cells express similar levels of the molecule. Am I right ? Or do I need to consider autofluorescence ? One possibility would be to change the settings (PMT) so that autofluorescence of both cells falls within the same range, but I do not like this solution......... The problem is even worst when comparing T cells to dendritic cells or macrophages ... Thanks , Oberdan LEO
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