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Due to the visual aspects of the staining, discrimination of infiltrating cells was not possible.
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Annexin V/PI co-staining allowed discrimination between early apoptosis (only Annexin V stained cells), late apoptosis leading to secondary necrosis (double stained cells) and primary necrosis (only PI-stained cells).
After an incubation period of up to 7 days, the cells were stimulated with PMA and ionomycin and harvested, stained for discrimination between live and dead cells and immunostained for CD3 and several cytokines.
While the addition of vimentin to CD9 staining slightly improved discrimination, we doubt that both markers need to be used routinely in the clinical setting.
Thus, double staining enables discrimination between intact cells (annexin V negative and PI‐negative), early apoptotic cells (annexin V positive, PI‐negative), and late apoptotic cells (annexin V‐positive and PI‐positive) or necrotic cells (without the characteristic cell integrity).
Cells were then washed twice and resuspended in 200 μL of DNA staining solution for cytometric discrimination of bacteria during leukocyte analysis.
A plausible explanation for the lack of discrimination of staining extent compared with intensity in our study would be increased sensitivity of the staining methods for the detection of positive cells.
Plasma membrane integrity was analysed by live dead discrimination after staining with propidium iodide (PI, Sigma) at a final concentration of 5 μg ml−1 for 15 min (Hostanska et al, 1996).
Yet, staining intensity (and thus discrimination between negative and positive) was lower with the PCH101 clones when compared with the 206D (PE) clone (Supplementary figure 1a c), which may be due to fluorochrome choice.
Staining with MTT allowed simple discrimination between viable and dead intestinal organoids using bright-field microscopy.
For C×43 staining a global threshold enabling discrimination between background and C×43 signal was selected.
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