Bioanalyzer on pre-prepped ChIP-seq samples

[purplesock42]

Hey All,

I have been trying to QC my user submitted ChIP-seq samples via Bioanalyzer. Multiple different PIs have submitted samples which have been supposedly IPed and yet the Bioanalyzer trace shows their material to all be around 1kb (making size selection at the end of the Illumina protocol at ~225bp unsuccessful).

One point of view that has been expressed is that incomplete removal of crosslinks would categorically prevent proper migration of the material, rendering Bioanalyzer inappropriate and unreliable for QCing the original submitted sample.

Does this make sense? Or is it more likely that the samples submitted were not fragmented to the right size?

Thanks

[Jiannan]

Hi, I am having the same problems. I think after reverse crosslinking for 6 hours, it should be enough to remove all the crosslinked proteins.

[NextGenSeq]

We always re-shear ChIP-DNA with our Covaris prior to library prep. Most Chippers use the Biorupter and it doesn't shear as uniformly to the desired size as the Covaris.