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Old 01-10-2011, 10:55 AM   #5
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Location: Dronning Maud Land

Join Date: Mar 2009
Posts: 129

The majority of the ChIP-DNA I get for library preps have a large quantity of ssDNA. The process of removing the cross-linking is rough and possibly denatures the sample. There are also some that think the IP also pulls down targets naturally bound to ssDNA (but I would think in the minority).

For all ChIP, the nanodrop was misleading for concentration. I now require dsDNA specific assays as initial QC/QA (picogreen, Qubit).

If there is a question of the origin of the DNA on the second bioanalyzer traces, dilute some and PCR with the Illumina primers. You should only see an increase of the material with adapters.
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