Why sonicate DNA to 200-800bp?

[Melissa]

Hi guys,

I don't understand why Illumina recommends an insert size of 200-800bp for Truseq ChIP library preparation when the protocol selects only 250-300 bp fragments for sequencing. Since Truseq index adaptor is about 63 bp long, only DNA fragments around 124-174 bp are sequenced. In that case, shouldn't we sonicate the DNA fragments around 150bp?

Cheers,
Melissa

[Melissa]

I emailed Illumina tech support and the answer I got is rather vague. 200-800bp is recommended because it can be hard to sonicate ChIP dna to a smaller size. Seems like there is nothing wrong with using sonication size of 150bp.

[RNAarecrazy]

yes, we routinely sonicate to size 150-200bp for chip-seq.

[Melissa]

Thanks for the info