ChiP-seq - ThermoScientific Pierce Kit - possibly overfixed DNA

[Elsie]

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.
thanks.

[nucacidhunter]

If you prepare libraries with DNA samples described there, there will be two downstream issues. Firstly, accurate quantification of libraries for clustering with multiple peaks is difficult and inaccurate quantification can result in over or under clustering which will affect read number or quality or both, although that might be considered sequencing service provider problem. Secondly, small fragments are more efficient in cluster formation in comparison with large fragments and more of your reads will be from sequencing smaller fragments.

[Elsie]

Thanks Nucacidhunter, your comments are exactly what I suspected would happen downstream. Unfortunately these libraries are not going to be remade so I will just have to work with what I've got. Thank you.

[nucacidhunter]

One suggestion I have reluctantly because I have not tried it myself, is shearing pool of your DNA with a Covaris set to 150-200 bp if you have access to one. In this case smaller fragment would not shear any further but larger fragments should shear. You can try shearing a cheap source of DNA to your current peaks. Pooling them to emulate your current ChIP DNA pool and trying shearing on them first to ensure that it works and that also will allow you to optimize if things does not work out at first go.