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Is there any way to determine the number of integrated shRNA copies in my cells?

There is no easy method to determine the number of integrated copies of shRNA. The best approach is to titer the virus and start with a known MOI. For example, if one uses a MOI of 0. 3, it is more likely that the cells have a single shRNA copy. In-house we use a Poisson distribution that shows the expected percentage of cells that show a given copy number for a given MOI. This can help to determine what to expect in an experiment.