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A chromatin immunoprecipitation (ChIP) experiment for RNA polymerase II (RNAP2) is carried out, specifically to tell...

A chromatin immunoprecipitation (ChIP) experiment for RNA polymerase II (RNAP2) is carried out, specifically to tell the difference between RNAP2 bound to the promoter and RNAP2 that has escaped the promoter but has not yet begun to fully elongate (RNAP2 serine 5 phosphorylated).

Describe two issues that might come up when designing your experiment to obtain the type of data you desire. Also provide a solution to address these two issues.

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