DNA Microarray Core Facility

Agilent Bioanalyzer RNA Quality Check FAQ

Frequently Asked Questions

RNA Quality Check

  1. How much RNA do you need for a quality check?
  2. What is the detectable range of RNA concentration for the RNA quality check?
  3. What should I look for in the Agilent Bioanalyzer RNA Quality Check result?

RNA Quality Check

Question: How much RNA do you need for a quality check?
Answer: Please give us 3 μl of each RNA sample in 0.5 tubes. 1ul is run on the Agilent Bioanalyzer (but we might need to rerun the sample in case it didn't run well the first time). For quality check prior to microarray analysis 1 μl is also needed to measure concentration and absorbance ratios on NanoDrop.

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Question: What is the detectable range of RNA concentration for the RNA quality check?
Answer: NanoChip: total RNA: 5-500 ng/μl; mRNA: 25-250 ng/μl.
PicoChip: total RNA: 0.2-5ng/ul; mRNA: 0.5-5ng/ul.

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Question: What should I look for in the Agilent Bioanalyzer RNA Quality Check result?
Answer: For information about the RNA Ladder we are using, check here.

For total RNA:

RNA quality: For microarray analysis the RIN score should be greater than 7. The ratio for rRNA 28s/18s is also an indication of RNA quality. The ideal ratio is 2, a low ratio is a indication of degradation of the total RNA. On the gel image and the graph, the 28s and 18s should show up as 2 sharp bands/peaks.

RNA concentration: The Agilent RNA quality check can give you an estimate of the RNA concentration, however, we have found it is not as accurate as the NanoDrop measurement. If concentration is what you're concerned about, you are welcome to double check it on our NanoDrop spectrophotometer. Click here for more information.

For mRNA:

rRNA contamination: the percentage of rRNA in your sample. The ideal number is <5.

RNA concentration: The Agilent RNA quality check can give you an estimate of the RNA concentration, however, we have found it is not as accurate as the NanoDrop measurement. If concentration is what you're concerned about, you are welcome to double check it on our NanoDrop spectrophotometer. Click here for more information.

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