How soon after incubation with Cyto-ID® autophagy dye would the samples need to be analyzed by flow cytometry? The user manual recommends following 30 minutes incubation. Is it advisable to temporarily store samples on ice before they are analyzed?

One can store the samples on ice for a short period of time to extend the period of optimal staining. The general rule of thumb is to minimize the time live cells are exposed to any dye. Storage conditions might induce a hypoxic state, hypothermia and other stresses that can induce autophagy.