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The Agilent Bioanalyzer is used for RNA, DNA and protein analysis.
High sensitivity DNA chip
We are running Illumina sequencing samples on the bioanalyzer with the DNA high sensitivity chip. To select this option for ordering pick 'Illumina prep DNA' for nucleic acid type.
Total RNA quality (Nano chip and Pico Chip)
The Bioanalyzer can be used to look at total RNA quality by observing the 18S and 28S ribosomal peaks and their ratio, or 16S and 23S peaks of prokaryotes. The 28S/18S ratio should be 2, but often is much less with the RNA being of good quality. More important than the ratio is the degradation in the peaks. Look for the amount of degradation between the 18S and 28S peaks and the area smaller than 18S. Software now gives a RIN number to give a quality assessment of the total eukaryotic RNA. The RIN number does not work for prokaryotic samples and samples with extra ribosomal peaks such as from chloroplasts before the 18S peak. There is a new assay for plants which compensates for those extra ribosomal peaks. Pick 'Plant total RNA' for nucleic acid type during submission to let us know to run this assay.
mRNA quality (Nano chip and Pico Chip)
The bioanalyzer will also look at mRNA. You can see contamination with ribosomal RNA and the approximate the size range of the mRNA.
The bioanalyzer also quantifies RNA, but it is not always accurate. It is best to quantify RNA before running on the bioanalyzer, and run all samples with the same concentration to make a good sample-to-sample comparison. The accuracy range of the RNA 6000 Nano chips is from 100ng/ul to 500ng/ul. Overloading or underloading will give inaccurate concentration results, or may clog the channels. The accuracy range of the Pico chip is 50 pg/ul to 5000 pg/ul, however this chip is much more sensitive to contaminants than the Nano chip. Supply sample in water. Avoid salts and particulate by using dust free gloves and filter free tips if possible when preparing samples.
There are also DNA chips, protein chips available for use on the same instrument. There is also a flow cytometry option that we do not have. You can find more information on the web site at Agilent.