What stain should I use to analyze apoptosis in flow cytometry?

A good option for analyzing apoptosis is an Annexin V/PI assay. Annexin V can be conjugated to a variety of fluorophores such as FITC and works by binding to phosphatidylserine (PS) residues, which translocate from the inner to the outer leaflet of a plasma membrane during apoptosis. Cells undergoing apoptosis will thus stain positive for Annexin V. Meanwhile, PI (propidium iodide) binds to DNA and stains dead cells.

Using the Annexin V/PI assay can distinguish between early apoptotic cells, which stain Annexin V+/PI-, and late apoptotic cells, which stain Annexin V+/PI+. Live cells stain negative for both Annexin V and PI. However, it is important to note that necrotic cells can stain both Annexin V-/PI+ and Annexin V+/PI+.