Hi, I would appreciate so much your input to my problem/question. I extracted genomic DNA from yeast for whole genome sequencing (illumina Hiseq technology), and digested the prep with RNAse A. However, after running an agarose gel to see the quality of my extraction (genomic DNA is ok) I also saw a strong band of 75 bp in size. This is a small fragment, so I am thinking that this is most likely digested RNA. Now, my question is if this digested small RNA would interfere with the Illumina sequencing process. I understand that the Illumina sequencing generates fragments larger than 200 bp in size or so. Thank you.
No, RNA will usually not interfere with library preparation in general as all library prep methods work only on DNA. The only problem it might cause is that you overestimate the amount of DNA in your sample if you use UV extinction based quantification methods.
More critical for success is the library prep method you use. I strongly recommend TruSeq PCR-free library, if you can get ~2ug DNA, with a fragment size of 800bp.
Yeah, the Qbit is one of the reliable methods. So you should have no trouble.
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