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Old 02-04-2015, 01:55 PM   #1
Melissa
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Question Why sonicate DNA to 200-800bp?

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?

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Melissa
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Old 02-12-2015, 10:03 AM   #2
Melissa
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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.
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Old 03-07-2015, 09:25 PM   #3
RNAarecrazy
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yes, we routinely sonicate to size 150-200bp for chip-seq.
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Old 04-08-2015, 09:50 AM   #4
Melissa
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Thanks for the info
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