Our lab deals with mRNA expression profiling studies using both cDNA and oligonucleotide microarrays. For these studies, proper RNA handling and RNA quality evaluation play a critical role in our daily laboratory work. Several months go we bought an Agilent 2100 Bioanalyzer to improve the RNA quality assessment and sample throughput. Our experience with this machine so far has led us to believe that this was a good investment. First of all, using the Bioanalizer to evaluate RNA samples does not require any gel separation or photodocumentation. In addition, the Bioanalyzer uses as little as 5 ng of RNA for a single measurement. This is a very significant savings, in terms of the amount of sample used for analysis, which is important when working with a limited number of cells. The Bioanalyzer utilizes Agilent’s Lab-on-a-Chip technology, thus sample handling is limited to loading. Results of the RNA analysis are presented by user-friendly software as a gel-like image or as a diagram. In both cases, the integrity of total RNA can be easly assessed by evaluation of the 18S and 28S units of ribosomal RNA. In the case of messenger RNA, there is the possibility to detect ribosomal RNA contamination. The detection time is in the range of minutes, which is extremely fast compared to the hours we used to spend running gels to analyze RNA.
What I really like about this machine is that gel-like images and electropherograms can be easily pasted into presentation and publication files. Data can be also converted into plain text which is useful for comparisons and archiving as well as data mining. Another advantage is the size of the instrument. Including the dimensions of the standard PC that accompanies the machine, the Bioanalyzer can easily be placed on the lab-bench.
Of course, the convenience of the Bioanalyzer also has its price. The RNA chip used to analyze samples can not be regenerated, therefore one has to buy new ones. One must also be careful to check the expiration date of the RNA marker (which has a shelf-life of six months) since it serves as a reference for the RNA measurements. During our work with the Bioanalyzer, we encountered few problems related to the interpretation of results. On a few occasions, the ribosomal RNA peaks were clearly visible but they were unusually broad when compared with reference plots. This would suggest RNA degradation, but the bands on gel images remained sharp. We would recommend that people be careful with these kind of RNA samples in terms of further usage for hybridization experiments.
In summary, I would not hesitate to recommend the Bioanalyzer from Agilent for any laboratory that performs RNA preparations frequently. There are several research groups which use this instrument on a daily basis and so far I have heard mostly positive opinions. This device can be also used for DNA and protein qualitative and quantitative estimations with similar convenience and speed as for RNA measurements.
Michal Janitz, M.D.
Max Planck Institute for Molecular Genetics