I have probably a very simple question, but I need some help exploring my ChIP-data. I have three different sample: 1. untreated 2. treatment with stimulant 3. treatment with inhibitor
First thing I want to know is where do I see increased binding in 2 compared to 1. From this I want to obtain a list of genes where binding of protein of interest is increased in a new file. Then I want to use that file to see where binding is decreased after 3 to find out at which genes binding is decreased after treatment with the inhibitor.
The idea of the experiment is that we treat the cells with a stimulant that induces protein binding and then we follow the stimulant with an inhibitor to see where protein binding is decreased due to the inhibitor and have a list of genes where the protein binding is not disturbed by the inhibitor vs where it is disturbed.
Does anyone have some guidance how to approach this? I am a complete novice when it comes to bioinformatics and I could use some pointers.