Bioanalyzer (Kathryn)

The bioanalyzer can be useful for quantifying and quality checking double stranded DNA, RNA, and proteins. This method of gel electrophoresis will tell you both fragment size and concentration for each fragment, using up only 1 uL of sample. The reagents and chips are expensive (for the High Sensivity chips, ~$100/11 samples/single use  chip), and have limited shelf life (4 months or less).

Rieseberg lab members have used this machine to check the quality of sequencing libraries and cDNA for microarray expression analyses. Various DNA and RNA kits are available, depending on what you want to measure, and their specs are at the bottom of this post.

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Quantifying DNA (Dan E.)

This post is about quantifying DNA samples in the Rieseberg lab, i.e. using the tools we have available to us in our lab in the Biodiversity building as of November 2011.

There are three ways to quantify the amount of DNA in an aqueous solution (e.g. DNA dissolved in water or TE):

  1. Nanodrop (spectrophotometry).
  2. Qubit (flourometry).
  3. Agarose gel with EtBr (also fluorometry -> UV lightbox + your eyes = fluorometer).
  4. (There is also the BioAnalyzer – I’m going to ignore that here and focus on methods to measure high mw genomic DNA).

These methods have different benefits and limitations but they are all valid and useful.
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