I want a dye that can track cells similar to CFSE, but excited with 405 nm violet laser. What is available?
CellTrace Violet and CellTracker Violet BMQC work in the same way as CFSE, but are efficiently excited with the violet laser. They are comparable to CFSE in terms of cell retention, and has been used for tracking cells with microscopy as well as flow cytometry.
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I want to do a cell migration study for around 4 hours and need to fluorescently label the cells with a dye. What do you recommend?
Calcein, AM and FDA (fluorescein diaceate) are examples of some dyes used for this application. Since these dyes are not incorporated or covalently attached to any cellular components, they may have a short retention time as some cell types may actively efflux the dye out of the cells. The CellTracker and CellTrace dyes include either a mild thiol-reactive chloromethyl group or amine-reactive succinnimidyl ester group to allow for covalent binding to cellular components, providing for better retention. As with any reagent, one should empirically determine retention times for the cell type used.
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I labeled my cells with Calcein, AM, but when I imaged the next day, there was no fluorescence from Calcein. Why?
Calcein, AM is a good choice for cell tracking and as a general cytoplasmic stain. However, it doesn't bind to anything and may be actively pumped out of the cells within a couple hours, which is likely what happened. The retention of Calcein within live cells is dependent upon the inherent properties of the cell type and culture conditions.
For long-term imaging, you may wish to consider a reactive cytoplasmic stains such as CFDA, SE or the CellTracker and CellTrace dyes.
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Can the CellTracker dyes be fixed?
Yes, the CellTracker dyes react with any accessible thiol part of the protein and can be fixed. However, some CellTracker dyes may be attached to small metabolites that can leak from the cell following permeabilization. This can result in decreased fluorescence.
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I stained two populations of cells, one with CellTracker Green and the other with CellTracker Red, but it looks like there may be crossover of the red dye to the green cells. What is going on?
One possibility is that there is spectral bleedthrough between the dyes. Be sure to check the single-color samples by imaging the red cells in green and imaging the green cells in red, using the optimal imaging settings for the other color. If you see bleedthrough with these controls, then you will have to reduce the dye label concentration to reduce the brightness of the dyes, or choose dyes that are farther apart spectrally. If the issue isn’t bleedthrough, another possibility is that the cells were not adequately washed after staining, allowing some unincorporated dye to remain and label the other cells after they were introduced. Extending washes and wash times should help with this.
Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.