We have performed CHIP assay using magnetic bead CHIP assay kit (Cat: 9003, CST) and got desired band in agarose gel electrophoresis after the chromatin digestion. But when we went for RT-PCR did not get proper data. Can somebody suggest me how to troubleshoot this problem? After immunoprecipitation and DNA purification we got the DNA concentration 18 ng/ul. We did not get any amplification even in 2% input sample.
Using similar kit, #56383 from cell signalling company and also following a similar protcol from Abcam X-Chip, i am always getting "DNA too low to be detected".
How did you get " concentration 18 ng/ul"?
Did you check if the fragmentation is proper and not over fragmented by the enzyme? This may lead to NO amplification even in 2% Input control.
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