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Old 05-08-2017, 09:57 AM   #2
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Location: Bay Area

Join Date: Jun 2012
Posts: 118

One of the miRNA methods would probably work. The RNA ligase used in most preps can also act on ssDNA. You might need to do a PNK treatment first. I haven't looked at the library prep chemistry in a while, but they might rely on the miRNAs mostly being 5' phosphorylated.
You could sequence also sequence the amplicons. You'll be enriched for the primer sequences at the 5' ends if you do a non-nextera prep. You won't know the 3' ends, but you can make an educated guess by looking at Tms or feeding the assembled amplicons through primer3
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