ChIP qPCR analysis - (Jul/27/2006 )
Can anybody tell me how to analyze ChIP-qPCR data? How to show the data in the paper? Thanks!
You need to correct data for the input DNA (like an HK gene in the qPCR) and then set the value foe the control at 1 and express the other values as % of recruitment of the TF you used to do IP.
I amplify the target sequences from the precipitated chromatin and then an houskeeping gene (I like GADPH) from my input. Then I follow the guidelines from the handbook from Applied Biosystems about RT-qPCR and I get some values relative to the HK gene. At this point I normalize to the value of the chromatine I pulled down with my transcription factor and that's it. In this way I have all the sequences I IP set to one and the non specific looks very small. Also the stdev looks small and nice. You can also have a look at some papers in which people showed chromatin IP and see how they show the data. One of the most experienced labs in this is Bruno Amati's lab: if you search for some papers from his lab, you will read about this "quantitative ChIP". I hope it helps.