Yes, you can use any of our three Cell Meter™ Autophagy Assay Kits (Cat# 23000, 23001, 23002) with a flow cytometer, fluorescence microscope or fluorescence microplate reader. From our experience Cat# 23002 showed the best response when used in flow cytometric analysis, then Cat# 23001 and finally Cat# 23000.

Below is a sample autophagy assay protocol using a flow cytometer:

1. Incubate Jurkat cells in RPMI medium with 10% FBS (control) or in 1X HBSS buffer with 5% FBS (starved) for 16 hours at 37°C.  
2. Spin down both the control and starved cells, and then re-suspend in 1X HBSS buffer.
3. Prepare dye working solution by diluting 20 µL of Autophagy Blue™, Autophagy Super Blue™, or Autophagy Green™ (depending on which kit you are using) with 10 mL of Stain Buffer.
4. Stain cells with dye working solution at room temperature for 20-30 minutes.
5. After staining, spin down cells and wash with 1X HBSS buffer.
6. Analyze cells with flow cytometer.
   1. Autophagy Blue™ has fluorescence excitation and emission at Ex/Em = 335/520 nm
   2. Autophagy Super Blue™ has fluorescence excitation and emission at Ex/Em = 335/520 nm
   3. Autophagy Green™ has fluorescence excitation and emission at Ex/Em = 485/530 nm