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I'm doing some library preps for DE analysis, and I'm curious if this kit, which selects for mRNA will also capture viral RNA? I'm hoping to do DE analysis between infected and uninfected samples so I'm hoping I can determine infected status from the sequences as well. Any idea?
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You might capture viral sequences by chance, due to cross hybridization events? By design you will not sequence viral sequences from poly-A enriched samples.Last edited by luc; 05-18-2016, 05:37 PM. -
Thanks luc for the response.
If all retroviral RNA transcripts are capped on the 3' end, and cleaved and polyadenylated on the 5' end, should I expect those sequences to be included in the poly-A selection?Comment
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I do not know enough about viruses - hardly anything. Are there 3' caps ? (I am only aware of 5' caps. )
With the poly-A enrichment you can remove most of the rRNA (usually more than 90% of your total RNA sample) from your sample. If you can somehow selectively A-tail your viral sequences (and not also the rRNAs), this might be workable.
Very likely ribo-depletion protocols would be a good way to remove the rRNAs in your case.Comment
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