ChIP - (Oct/17/2006 )
I am doing ChIP for a transcription factor. how do we get a clue of what promoters might bind to the TF? How do we start working it out?ultimately i am planning to do a Chip on a chip but how do we know that the iniital ChIP has worked?
Don't you know the consensus which your TF binds to? Don't you know any of the promoters regulated by this TF? Isn't there anything in the literature?
In order to understand whether the ChIP worked or not, I don't see any other way that doing a real-time comparing the amplification you get from IP with non-related Ab and from IP with specific Ab. What you could do is to IP also another TF (of which you know the promoters it binds to) and use this to check by real-time whether the ChIP itself worked. But this won't tell you whether you specific Ab worked...