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What would be the cause of variation in knockdown level between replicates?

If plates are true biological replicates (same cells, split same time, treated the same) then the knockdown differences between replicates might very well simply be experimental variation caused by technical details (pipetting, handling, gel loading etc. ) If different cell lines are tested or even the same cell line passaged at a different time or under different circumstances, then the differences might be intrinsic to the nature of these varying factors. For instance, differences in cell cycle status as well as cell line differences could account for the knockdown variation.