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Old 02-16-2012, 10:12 AM   #8
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279


For library prep we use the Qubit values exclusively as long as it passed all the QC checks. I went through our database of results and pulled out the samples tested by both Nanodrop and Qubit. We see the following correlation (n=43) for percent quantity (Qubit/Nanodrop):

Median = 68%
Min = 38%
Max = 84%
STD = 8%
25th Percentile = 63%
75th Percentile = 70%
R-square = 87.4%

If you are only seeing 3-7% of nanodrop I'd want to ensure you have an RNA free prep and that it is not degraded. We have seen that degraded (smear on a gel) shows much lower concentration by qubit/picogreen than high molecular weight DNA at the same concentration as measured by nanodrop.
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