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ChIP densitometry - (Apr/13/2008 )

Hi everybody!, I've carried out a ChIP of acetyl H3 and H4 histones after treatment with TSA. I'm doing qRT-PCR but I've also performed conventional PCR. I've done a densitometric analysis of the bands obtained in an agarose gel after PCR and I have some doubts with the analysis data method. I've been thinking on normalizing (by dividing) the value of each IP band with the corresponding Input, is this correct??. I mean, I'd like to do a figure with the gel and a graph above it, each gel lane with the corresponding column of the graph just above, but if I use "my method", the Input lanes won't have any column. Do you know any reference of a paper with the same experiment??. Do you think is right?

I hope you'll understand me in spite of my poor English.

Thank you in advance



actually I do the calculation the same way you do. The input amount must be anyway the same/similar since you adjust the DNA amounts before the IP, right. That`s the control. The normalization makes the quantification more exact. I cannot reference to a specific paper (sorry), but I remember that I have seen papers saying that the input is 2, 5 or 10% and showing one input band.