Department of Botany & Plant Sciences

Bioanalyzer Best Practices

Bioanalyzer Best Practices

In order to facilitate more expedient and accurate Bioanalyzer sample quantification the Genomic Core asks users to follow the guidelines below.

  1. Before submission use the Qubit to obtain an accurate determination of sample concentration in ng/ul. The Qubit is preferable to NanoDrop due to higher sensitivity and specificity. The Nanodrop quantifies both DNA and RNA at the same time leading to inflated concentrations and dilution errors that may result in needing to re-run samples. Additionally, the sensitivity of the Nanodrop is poor at values less than 20 ng/ul. (Note: Suggested changes to form for Bioanalyzer change units to ng/ul and add selector box for instrument Nanodrop/quibit).
  1. On the Bioanalyzer submission form, enter the concentration values obtained from the Qubit in ng/ul (The box will allow text to be entered as well as numbers.) These values will allow more accurate dilutions. (May not want to keep but I entered as a suggestion. Alternatively, we could change the value on the submission form, but I don’t know if that is difficult)
  1. Provide a small aliquot of the sample to be run on the Bioanalyzer. A three microliter aliquot is more than enough to dilute for a Bioanalyzer run and leave a remainder to re-run the sample if necessary.


Unique to RNA Bioanalyzers

3 chip choices: Nano, Pico, Small

Nano (12 samples): 25-500ng/ul (in practice, more like 40-500ng/ul),

or 25-250ng/ul mRNA

Eukaryotic Total RNA assay

Nano mRNA assay (no RIN given)

Prokaryotic Total RNA assay

Plant RNA Nano assay


Pico (11 samples): 200-5000pg/ul Total RNA,

or 500-5000pg/ul mRNA

Eukaryotic Total RNA assay

Pico mRNA assay (no RIN given)

Prokaryotic Total RNA assay

Plant RNA Pico assay


Small (11samples): 6-150nt

50-2000pg/ul purified miRNA,

or 1-100ng/ul Total RNA,

or 1-20ng.ul purified small RNA,

or oligonucleotides 100-2000pg/ul

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