High %rRNA in NuGen Encore invert libraries
We recently did a number of library generations using the Nugen Encore kit. The samples were from flies, Drosophila melanogaster; extractions and library preps were done by very experienced staff.
After Illumina HiSeq sequencing and Tophat/Cufflinks alignment, we found that the proportion of the reads due to rRNA was between 50%-84% (median 60.5%, number of samples = 90). We were surprised because we thought rRNA depletion was supposed to be good with this kit.
When we went back to the Nugen website, we found there was a new video (near the bottom of the page below). Around 2:15 into it you will see the attached chart, which notes the kit doesn't deplete rRNA very much for invertebrates.
We learned the hard way. If you work with a non-mammalian system, be aware of this issue.
After Illumina HiSeq sequencing and Tophat/Cufflinks alignment, we found that the proportion of the reads due to rRNA was between 50%-84% (median 60.5%, number of samples = 90). We were surprised because we thought rRNA depletion was supposed to be good with this kit.
When we went back to the Nugen website, we found there was a new video (near the bottom of the page below). Around 2:15 into it you will see the attached chart, which notes the kit doesn't deplete rRNA very much for invertebrates.
We learned the hard way. If you work with a non-mammalian system, be aware of this issue.
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