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Old 01-22-2014, 07:45 PM   #2
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Default small rna ligation of 5'adapter

Sometimes it's difficult to visualize a doubly ligated small rna product (rna with a 3'ligated and 5'ligated adapter). The ligation efficiencies are pretty low, making it difficult to visualize on a gel. I would try running your sample on a bioanalyzer. You could also make a synthetic control RNA (with 5'phosphate and 3'OH) to check your 3 and 5'ligations. You'll be able to see this much better than small RNA isolated from cells or tissue.

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