CellTrace™ Yellow Cell Proliferation Kit, for flow cytometry, 20 Assays - FAQs

We have not tested the use of the CellTrace reagents for co-culture applications. In theory, this may work, but you would have to test this on your cells of interest.

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A single broad peak is usually caused by using too high a concentration of dye and/or too long an incubation time.

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The dyes provided in the CellTrace Proliferation kits are amine-reactive dyes that are considered general cytoplasmic stains. They may bind to various membrane proteins, organelles as well as components in the cytoplasm. They are not known to localize in any specific organelles.

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A single broad peak may be observed if the dye concentration used is too high or if the dye incubation period is too long. We recommend reducing the amount of dye used and/or the incubation period.

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We recommend using the CellTrace Yellow Dye if you have either a 532 or 561 nm laser available on your flow cytometer and you want to use the other lasers and channels for other commonly used fluorophores.

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Using either a 532 or 562 nm laser, CellTrace Yellow Dye may be detected in the PE/PI emission channel using an Attune NxT Acoustic Focusing Cytometer with 561 nm excitation and a 585/16 nm bandpass emission filter.

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We provide the CellTrace reagents in small aliquots and strongly recommend discarding any unused DMSO/dye stocks. The CellTrace reagents have acetyl groups to cap the charges on the dyes to make them cell permeant, and succinimidyl ester amine-reactive moiety to allow for covalent attachment to cellular components for long-term retention. Both acetyl groups and succinimidyl esters will readily hydrolyze if any water is present during storage. DMSO is hygroscopic and thus readily absorbs water from the atmosphere. If you must store your dye stocks, you will need to use a good quality, anhydrous DMSO stock that has not been opened often and store the vial within an air-tight container containing some desiccant to keep the DMSO/dye stock solution anhydrous during storage.

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Here are some tips to obtain uniform staining and a bright, unstimulated parent generation peak:

Dissolve the CellTrace dye stock immediately before use in the DMSO provided in the kit or in good quality, anhydrous DMSO to obtain the best reactivity and cell permeability.
Stain in PBS or other amine-free, protein-free physiological buffer. Do not stain in medium.
Start with a single-cell suspension and gently agitate the cells during staining.
Quickly remove the unbound dye by incubating the cells in ice-cold media for 5 minutes and then wash twice more with pre-warmed media.
Include a dead-cell stain in the assay and gate only on live cells.
Analyze as many cells as possible from each sample.
Use a low flow rate for analysis on hydrodynamic focusing cytometers.
A good staining concentration for the CellTrace dyes is generally within 1-10 µM, but the optimal concentration for a particular cell type will vary. Observe your cells in a stain dilution series to determine the optimal concentration for your cells.
Some cell types may take up dye with a broad staining intensity distribution. If this is the case for your cells, then you will need to do an initial sort of the stained, unstimulated parent cells to select for a narrow peak distribution.

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We provide the CellTrace reagents in small aliquots and strongly recommend discarding any unused DMSO dye stocks. Some of the CellTrace reagents have diacetate groups to cap the charges on the dyes to make them cell permeant, and some have succinimidyl ester amine-reactive groups for long-term cellular retention. Both diacetates and succinimidyl esters will readily hydrolyze if any water is present during storage. DMSO is very hygroscopic and thus readily absorbs water from the atmosphere. We do not recommend storing stock solutions of CellTrace reagents because storage of the product in solution will inevitably lead to partial or complete loss of reactivity.

CellTrace Cell Proliferation reagents are all cell-permeant dyes that are cleaved by intracellular esterases to yield highly fluorescent compounds that also covalently bind to cellular amines, attaching the dye to various cellular components and providing a very stable signal. These reagents show little cytotoxicity with minimal observed effects on the proliferative ability of many cells.

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This is not recommended. When these stains bind to DNA and RNA, they may affect the normal function of the nucleic acids, disrupting transcription, as well as replication. Other reagents, such as CellTracker dyes or Qtracker reagents are more optimized for tracking without disrupting normal activity. If a nuclear label is still desired, though, and the cells are mammalian and non-hematopoietic, CellLight nuclear reagents can transiently transfect cells to express GFP or RFP on a nuclear-expressing protein for up to several days without affecting function.

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Please see this Web link (http://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-tracing-tracking-and-morphology/cell-tracking.html) to help you choose the right option for your application. Start by planning how long you want to track your cells, then consider the mechanism of binding. Calcein dyes are very uniform in label and are good for short-term cell migration, but may be rapidly effluxed from some cell types. Lipophilic cyanine dyes, such as DiI, DiO, and similar dyes label cell membranes, don’t disrupt function, and can last longer, but have the potential to cross to other cells if membranes fuse. They are also lost upon permeabilization. CellTracker dyes are better for longer-term labeling, as they possess a mildly reactive chloromethyl moiety that allows covalent binding to cellular components. CFDA SE also covalently binds to cellular components. With all the reagents, their retention within cells is dependent upon the rate of cell division and the inherent properties of the cell (active efflux, membrane and protein turnover rates, etc.) and reagents that allow for covalent attachment exhibit longer retention than those that do not.

The longest-lasting and brightest options are the Qtracker reagents, which are taken up through endocytosis. These are so bright individual quantum dots can be detected, and are also robust enough to survive not only fixation and permeabilization, but even the heat and solvents used in paraffin processing.

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The key to good generational profiles with CellTrace reagents is starting with cells that are evenly labeled so that they have a tight coefficient of variance (CV) when run at time zero after labeling. If the peak is too broad, the generations will overlap each other and the series of peaks will become a hump. Even labeling can be achieved by starting with a uniform cell population (not a mixture of lymphocytes and granulocytes for example) as staining will be proportional to cell size. Cells are labeled rapidly, so you want to pre-dilute the dye and mix it into your cells rapidly. Be sure that the cells are not sitting in a clump in the bottom of your tube. The easiest way to do this is to make a 2x dye solution (1x = 1-10 µM) and resuspend your cells in a half volume of medium (no serum or BSA). Add the dye to the cells and invert a few times to mix. Gently agitate the cells during staining. Once the dye incubation is over (20 min, 37 degrees C), add serum or BSA (at least 1%) to scavenge any remaining unreacted dye. Spin down cells, wash 1x, and resuspend in complete medium. After a 10-20 min incubation to undergo de-esterification, cells are ready to be set up for whatever treatment you are planning. Be sure to keep a time zero control as you need to know where the first generation ran.

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-Measures data from single cells.
-Data are obtained for a large number of cells, generating a rich statistical analysis of cell populations.
-Because single cells are measured, it will reveal heterogeneity within a population.
-With the ability to multiplex, small sub-populations can be identified.
-Thousands of cells can be analyzed rapidly.
-It is ideally suited for blood samples and other cells in suspension.
-Data can be re-analyzed multiple times after acquisition.
-Flow cytometry files (FCS) can be archived.

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There are several applications, some of which include immunophenotyping, cell cycle analysis, apoptosis assays such as annexin V staining, CellEvent Caspase-3/7 assay, and TUNEL assay, cell viability, proliferation assays such as CellTrace assay and Click-iT EdU assay, measurements of mitochondrial potential with MitoProbe assays, and cell counting using counting beads.

Find additional tips, troubleshooting help, and resources within our Flow Cytometry Support Center.