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Old 04-18-2011, 11:35 AM   #1
brain_food
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Location: Philadelphia

Join Date: Oct 2010
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Default Majority of RNA-Seq library is mitochondrial RNA

Hi everyone,

We're currently attempting to make Illumina sequencing libraries with Epicentre's Ribo-Zero. Before sequencing, we TOPO-cloned our libraries and sequenced to clones (~20 per library) to get an idea of our libraries' diversity. Much to our dismay, we have found that a large portion of our clones (60-70%) map back to mitochondrial DNA. The predominant sequence bears a great deal of homology to the human gene Mt-rnr2-l (our libraries are from mouse). Has anyone else had similar difficulties with mitochondrial RNA? I've seen a few posts on this site where a higher mitochondrial RNA quantity has been referenced, but none addressing this problem specifically. I appreciate any help you can offer. Thanks in advance.
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