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Old 12-12-2016, 02:15 PM   #4
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,232

I do not know how rRNA depleted RNA profile should look like, but double depletion is expensive and not a good idea. The best practice is to do DNase treatment on total RNA extract before any downstream application. Genomic DNA contamination will be seen as high molecular fragments on RNA Chip. In your before treatment Bioanalyser trace if the peak at 100-150 bp are DNA they will be washed away during library prep and less likely will end up in RNA-Seq library. Generally DNA contamination will show up as higher alignment of reads to intergenic regions.
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