I use antimycotics such as Amphotericin to protect some of my cell cultures. I would like to use them with iPSCs, but I understand many cells are negatively affected by antimycotics. Has anyone tried using amphotericin with ESCs or iPSCs?
I have worked on adult stem cells but not on ESCs and iPSCs but my experience tell that it's not safe to use antifungals for stem cells and to be more specific for primary culture derived stem cells. They are never recommended. So a safer option is to avoid antifungals. I have grown cells successfully for years without antifungals and they worked very fine even in some case I have done stem cell culture for almost a year without any antibiotics and that worked fine.
I use amphotericin for perforating the cellular membranes for patch-clamping. Basically prolonged exposure of cellular membranes (>10 mins) causes small pores in cellular membranes. Therefore I think incubation of ESCs and iPSCs in amphotericin will likely result in membrane depolarisation and reduce viability.
If you are having issues with fungal contaminations, grow the cultures in parallel--one with and one without antimycotics. The former will serve as the backup for the latter.