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Old 05-29-2015, 01:09 PM   #2
cmbetts
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Location: Bay Area

Join Date: Jun 2012
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You have plenty of RNA, so your main issue is the low RIN scores. The key issue with low RIN RNA is that using common PolyA purification methods to isolate mRNA will lead to extreme 3' bias and other issues in your libraries. However, if you use an rRNA depletion method (Lots kits using either probe pull-down or RNaseH digestion are available) and skip any fragmentation steps in your library protocol, you should be fine.
I'd recommend checking out the literature for RNA-Seq from FFPE RNA and use their methods for guidance.
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