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Old 09-17-2010, 12:00 PM   #1
Location: San Francisco Bay Area

Join Date: Mar 2009
Posts: 89
Default Negative control sequencing

What are people in the field doing with respect to sequencing DNA captured in negative controls (IgG, preimmune serum, beads only, etc.)?

I hear very little about doing this. A labmate says she has talked with some labs doing major ChIP-seq projects and they always sequence the negative control.

Honestly, I don't always get measurable DNA from the neg control. One ChIP recently I recovered 480ng with the antibody and 7ng with the IgG+beads control and another was 580ng and 0ng. So, in these two cases it wouldn't even be possible. But many times I do pull down enough to make a library even though the enrichment of IP over negative is quite good.

Any thoughts/comments?
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