Should I make any modifications to the immunoprecipitation if I am doing a genome-wide analysis versus a targeted PCR analysis?
Yes, in the step: DNA isolation you should avoid DNA purifying slurry. DNA purifying slurry provides you with single-stranded DNA suitable for qPCR analysis. A more “traditional” DNA purification can be performed using the DNA purification Module (mc-magme-002) and Phenol / Chloroform /Isoamyl alcohol (PCIA) or columns (e.g. QIAquick). These purification methods provide you with double-stranded DNA ready for amplification, microarray and sequencing. Secondly, for genome-wide analysis after ChIP, you should start the ChIP assay with a larger amount of cells, when possible.
