Our core lab has been seeing unusual failures of size-selection when we prep ChIP samples for Illumina sequencing on our Beckman SPRI-TE robot. We generally size-select for 200-400bp. However, since the problem started, we've seen large post-enrichment bands at 500-700bp and little material in the 200-400bp range.
The problem appears semi-random (a few samples from each batch enrich normally) and does not seem to correlate with reagent lots. It is also confined to ChIP samples.
Our best hypothesis so far is that the problem is caused by undersonication- we ran a test of whole-cell extract with different sonication times and it suggests that more sonication ameliorates the problem.
Has anyone else seen this phenomenon, and do you agree with this hypothesis? Thanks!
The problem appears semi-random (a few samples from each batch enrich normally) and does not seem to correlate with reagent lots. It is also confined to ChIP samples.
Our best hypothesis so far is that the problem is caused by undersonication- we ran a test of whole-cell extract with different sonication times and it suggests that more sonication ameliorates the problem.
Has anyone else seen this phenomenon, and do you agree with this hypothesis? Thanks!
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