2100 Bioanalyzer From Agilent

I run a DNA Microarray Core Facility. We bought an Agilent 2100 Bioanalyzer about six years ago for analysis of RNA and DNA quality; we have never had any problem with this machine. The quality of RNA is very important in order to generate reliable results on expression microarrays. Very often, the amount of RNA available for the analysis is limited. The Agilent 2100 Bioanalyzer Kits are very sensitive. I routinely use the RNA 6000 Nano Kit and periodically the DNA 7500 Kit. In some critical situations, I was able to “stretch” the limits of these kits’ sensitivity and use less than the recommended 25 ng/ul of total RNA for the analysis (20 ng/ul worked), or 2 ul of diluted solution (with the concentration as low as 12 ng/ul) instead of recommended 1 ul, and it worked! Analysis of 12 samples can be done within 30 min.

The software is very intuitive and in general, user friendly. Data is presented in multiple formats: electropherograms, gel-like images for electrophoresis assays and results tables. Automatic and manual integration are possible; there are also tools for RNA fragment and smear analyses. The software permits opening data from multiple chips at the same time and overlapping of the electropherograms from different samples. These features allow comparison of different RNA (or DNA) preparations. Tables can be easily exported as Excel or text files for analysis and data mining. Each graph can be exported as an individual graphic file. Both tables and graphs can be easily copied into the clipboard and pasted into a word processing, spreadsheet, graphics or other application. Chip run reports can be printed as a PDF file.

Recently Agilent introduced Series II Kits and upgraded the software with a new tool which assigns an RIN (RNA Integrity Number) to each RNA sample. RNA integrity is no longer estimated by the ratio of 28S/18S ribosomal peaks, but by the entire electrophoretic trace of the RNA sample. This method is much more reliable than just ribosomal peaks ratio because it takes all RNA degradation products into consideration. The assigned RIN is independent of sample concentration, instrument and analyst thereby becoming a de facto standard for RNA integrity. The New Series II Kits (unlike the previous version) have a sufficient amount of RNA (or DNA) marker and are more user friendly in terms of packaging.

However, there are some disadvantages. Sometimes the software does not recognize a peak, and there is no way to force it to do it. Analysis settings can be changed only through the change of Assay Properties, and even this sometimes does not work. I would like to have more flexibility with the software and be able to indicate that there is a peak.

Another disadvantage is that chips are disposable, and no matter how many samples I need to analyze (sometimes only 2 samples), I have to use the whole chip, and therefore this analysis can be costly.

As a conclusion, I highly recommend Agilent 2100 Bioanalyzer for all laboratories that extensively work with nucleic acids. I am using this machine almost daily. Results are very reliable and reproducible. The Agilent 2100 Bioanalyzer saves precious material and time. Results of the analysis can be easily reported.