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Old 12-01-2008, 12:41 AM   #1
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Location: singapore

Join Date: Dec 2008
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Default Enrichement and Picogreen concentrations?

I am trying to do a ChIP for ChIP-Seq for a transcription factor (TF) that has no known binding site so far. I therefore can't check my enrichment by qPCR, and the only ways to QC my ChIP are western-blot and Picogreen qtification.
My western looks ok, but my Picogreen assays show not difference of DNA concentration between the control and my TF sample. Is it normal or should I see a difference. Is it a bad sign for the future ChIP-Seq experiment (too much background)?
I don't know what the fraction of my specifically enriched DNA should be: 1 or 50% of the amount of background DNA.
Anyone can help?
Thanks a lot!
drabe is offline   Reply With Quote
Old 12-01-2008, 12:13 PM   #2
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Location: Seattle

Join Date: Sep 2008
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Our picogreen concentrations of our ChIP and our Normal Rabbit IgG control can have very similar concentrations after sample prep. In our experience, the only way to know if a specific antibody worked (even if checked on western and pcr) is to sequence it and look at the differences. At that point the bad sign is if the peaks are at the same place when mapped to the genome.
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