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Old 05-18-2014, 08:33 PM   #1
Location: Australia

Join Date: Mar 2011
Posts: 85
Default ChiP-seq - ThermoScientific Pierce Kit - possibly overfixed DNA

Hi, newbie to ChiP-seq. I have two libraries prepared with the Thermo Scientific Pierce Magnetic ChIP kit, micrococcal nuclease digestion and sonication. QC from an Agilent Tapestation shows several low peaks at ~180bp, 363, 537 and 713bp respectively. Normal practice I'm told is to pick at 180bp and generate libraries from that. With such a tiny peak there, I could either:
- stick with 180bp, but not have much material to generate my library from
- pick from several peaks but then end up with fragments of different sizes, which could make the bioinformatics hard.

So would I:
- do the size selection and end up with a small amount of material
- skip the size selection (or rather have a broad size selection) and deal with the consequences later

Any advice appreciated, this experiment is unlikely to be repeated so I'll need to work with what I've got.

Last edited by Elsie; 05-18-2014 at 08:49 PM. Reason: Clarify question.
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