Carboxyfluorescein diacetate succinimidyl ester, or CFDA-SE, is a fluorescent dye used to stain and label cells to track their division. CFDA-SE is cell permeable, meaning it can cross the cell membrane and stay there for long periods of time. Once inside the cell, CFDA-SE reacts with amine groups on proteins to create a stable fluorescent label.

When a labeled cell divides, it shares proteins with its daughter cells, which become half as bright as the parent cell. This predictable decrease in brightness allows scientists to calculate the number of cell divisions using a flow cytometer and FCS Express or similar software.  

Tracking Cell Division

We use CFDA-SE in our lab to measure cell proliferation and T regulatory activity in our cell samples. You can use our CFSE labeling protocol in your lab to label cells prior to injecting them into mice to trace where the cells travel by collecting target organs, or combine the CFSE label with surface antigen staining in vitro to understand which cell population is dividing, just to name two examples.

Figure 1 below shows lymphocytes that have been labeled but have not been stimulated to divide. Figure 2 shows a sample of the same lymphocytes that we stimulated with phytohemagglutinin. These were analyzed using FCS Express (DeNovo Software) to create the best fit for the peaks, shown in green, and to determine the number of cells in each generation.

Using CFDA-SE in Your Lab

Here are all the materials you’ll need to get started with CFDA-SE labeling. For detailed procedures and additional notes and data, read our full CFDA-SE labeling protocol.

  • PBMC
  • Vybrant® CFDA-SE Cell Tracer Kit (Molecular Probes) or similar product from another vendor
  • Antigens (Such as our Tetanus toxoid or CMV Antigens)
  • PBS or HBSS
  • Culture Medium (X-VIVO 15® or Iscove’s Modified Eagle Medium with 10% human AB serum are suggested for culture of human PBMC)


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