Question: What sonication settings are recommended for shearing Exome libraries?
Answer: Exome libraries should be sheared to a median fragment length of ~225 bp prior to library generation. The following sonicators have been validated by 10x Genomics using the manufacturer specifications for achieving a 200-bp target peak size:
- Covaris M220 Focused Ultrasonicator (recommended, http://covarisinc.com/wp-content/uploads/pn_010166.pdf)
- Covaris LE220 Focused Ultrasonicator (http://covarisinc.com/wp-content/uploads/pn_010156.pdf)
- Covaris S2 Focused Ultrasonicator (http://covarisinc.com/wp-content/uploads/pn_010158.pdf)
For untested Covaris models, refer to the Covaris website for guidance (http://covarisinc.com/resources/protocols/#toggle-id-1).
We do not have experience using Bioruptor sonicators, however, if you choose to use a Bioruptor, the program settings should be tuned so the peak size is ~225 bp and the library traces look similar to those in the Exome Demonstrated Protocol.
Shearing conditions can be tested using genomic DNA diluted to ~3 ng/ul to determine appropriate settings.