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[labtek]

I am going to do ChIP on Chip (histone acetylation) to evaluate changes among cells under different treated conditions. As for the random amplification of IP DNA, should the same VOLUME of IP solution (regardless of DNA concentration), neg (from IgG IP) and input be used to do random amplification (Nanodrop can read low concentration of DNA. e.g IP ctrl gives15ng/ul , IP treated gives 20ng/ul, neg is 10ng/ul, and input is 50ng/ul)? Or should the same AMOUNT OF DNA (e.g 40ng DNA from each) be used to randomly amplify?

The same question for CHIP qPCR, should the same VOLUME of samples be used for qPCR? Or should the same AMOUNT of DNA be used for qPCR to evaluate enrichment?

Then, how to evaluate gene enrichment? If using the same VOLUME of sample, is it reasonable to compare the enrichment between the samples that using diff concentration of DNA? If using the same AMOUNT OF DNA, is it fair to reduce the amount of DNA from IP treated sample (the treated IP suppose to have higher amount of DNA then the untreated IP)? Can specific gene enrichment still be maintained at reasonable level if DNA of treated IP is reduce to equivalent to untreated IP ctrl?

Thanks for help.