I have used TBP protein antibody to immunoprecipitate between 2 conditions :
1 - RNA interferece for TBP (Treatment)
2- Without interference (control)
my experiment showing in Treatment condition TBP is not binding and in control TBP is binding. I want to prove this by chipseq analysis.
I performed Chipseq analysis using Bowtie for alignment , MACS2 for peak call and macs2 bdgdiff for differential peak beween control and treatment , i got 3 peak files common , treatment over control , control over treatment .
My question is , how can prove in Treatment TBP is not binding and in control TBP is binding . What next method i have to use ? I used MEME-chip and Rsat to find TATA region but couldn't found in both treatment and control .
can any expert suggest ?