I would like to do some ChIP-on-chip experiments using Affy promoter arrays to check for binding of a TF after treatment.
People at Affy say that I will need to run at least 2 chips per condition (one neg ctrl IP sample (IgG or No Ab) and the Ab against the POI), to correct for unspecific IP.
Now I was thinking, since my TF is only activated after treatment, I already don't expect to see much specific enrichment in untreated samples. So do you think I can just use the untreated samples as neg controls and express my data as enrichment relative to untreated samples? Or is it always necessary to have a neg. control from every single ChIP sample?
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Untreated sample as negative control for ChIP-on-chip?
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