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Old 02-18-2011, 01:18 PM   #1
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Location: Boston

Join Date: Feb 2011
Posts: 3
Question ChipSeq library construction from tissue and DNA purity issues


we are currently trying to construct a ChIP-Seq library from a tissue sample. To complicate things, the transcription factor we would like to assay for is only expressed in a fraction (maybe 3% or so) of the cells present in the sample.
I am able to get about a 5fold enrichment for a candidate gene by ChIP-qPCR.
However, I am concerned about going forward with library construction because of the signal/noise ratio I may have to expect. Furthermore, my 260/280 ratios of the chipped DNAs as by Nanodrop suck (~ 1.3 after ProK digest and 2x PCI cleanup).
Has anybody ever done something similar?
Has anybody used Qiagen columns to clean up chipped DNA and found these to be OK even for small amounts of DNA? Would anybody perhaps have some other advice how to further purify the DNA?

Thanks for your help

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