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Old 10-03-2019, 05:58 AM   #2
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Location: Madison

Join Date: Feb 2019
Posts: 8

What RNA-seq method are you wanting to use? Typically, DNAse treatment in solution works fine, followed by rRNA depletion. Our library preps are done using a stranded system (any DNA reads would be "unstranded" or map to both strands). I have even taken to total nucleic acids sample, treated with Turbo DNAse, run rRNA depletion and then standard TruSeq Total RNA library prep. This should be done sequencing tomorrow or Monday; then we run RNA-Seq alignment and look at the stranded percentage. If there is excessive DNA in your samples, then percent stranded metric will be lower than 97% or so.
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