Should I assay for knockdown using individual colonies or pools of colonies after puromycin selection for shRNA?
With puromycin selection, it is best to pick individual colonies that are puromycin resistant and test several colonies in knockdown experiments. The reason for this is depending on the site of integration there could be variable levels of knockdown in different clonal populations. If you select with puromycin and use a heterogeneous population for your knockdown experiments, you may be diluting the rate of knockdown. However, this does not mean that knockdown cannot be detected using a heterogeneous population.