Bioanalyzer – RNA (Kristin)

Running a RNA Nano chip is very similar to running a DNA chip on the Bioanalyzer. However there are some things to keep in mind:

1. Clean everything with RNAse Away! before you start. I clean the chip loading stand as well as everything I am working with.

2. Make sure the reagents are at room temperature before you start to make the gel.

3. Before loading the chip, pipette 1.2 uL of each sample as well as the ladder into PCR tubes and incubate in the thermocycler for 2 minutes.

On the last point, I aliquot my samples into the PCR tubes and incubate them right before I load the gel. The instructions say to denature all the ladder in one go, but I have had better results when I denature an aliquot with my samples right before I run the chip.

Attached is a chip of 12 conifer leaf tissue extractions that worked out pretty well.

Conifer RNA Chip


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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