ChIP data normalization
Posted 31 December 2011 - 10:11 PM
I did H3K9me3-ChIP on samples from two different tissues.to compare the %Input at my gene of interest. One of the tissues showed reproducibly higher levels of H3K9me3 than the other tissue (n=4 independent replicates), but the interesting thing is that the positive control primer in the heterochromatin also gave consistently higher H3K9me3.
Now, the question is whether the ChIP values are indeed higher in both the gene of interest and the positive control primer (true positive), or whether the consistently higher values are caused by a systematic error in sample handling (false positive). I am thinking whether I should normalize my %Input with respect to the positive control primer to make the positive control score constant, and then read the new %Input at my gene of interest.
Do your positive control primers always have very similar values across biological replicates?
Or do people recommend any other methods of normalization?
Posted 02 January 2012 - 11:33 AM
Posted 12 January 2012 - 01:30 PM