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Advancing the quality control methodology,,,to assess isolated total RNA,,,and generated fragmented cRNA

at times the 18S and/or 28S bands of the total RNA were not clearly visible on the gels making the interpretation difficult. When running fragmented cRNA samples on MOPS gels it was often difficult to distinguish whether or not the samples were allowed a sufficient amount of time to fragment because of poor resolution. Problems with MOPS gels would lead to re-running of the samples on new gels, therefore wasting valuable time and money. The samples that should have failed would be caught by quality control measures later on in the process, but would ultimately cost the company money on reagents in the steps leading up to that.
The Agilent 2100 bioanalyzer combined with the RNA 6000 Nano LabChip Kit provides key advantages to running MOPS gels. The Agilent bioanalyzer data is easy to interpret and the chip runs on the bioanalyzer are less time consuming. It can take up to an hour and half to prepare the samples, run a gel, stain the gel, and take a picture. The whole Agilent process (sample preparation to saving the file) can be done in half that time. There is no improper staining and no shortened or lengthened run times. Also, because each chip has the capacity to run 12 samples, at approximately 30 minutes per chip, this makes the Agilent 2100 bioanalyzer a useful tool for high throughput screenings, especially with multiple bioanalyzers.
The goal was to find a new assay to be used to evaluate the quality of the total RNA and fragmented cRNA. This was needed because there was occasional inconsistency with the use of MOPS gels. The qualitative analyses should be as definitive and dependable as possible. Problems associated with MOPS gels in a high throughput environment may be due to user error. Common mistakes seen in the laboratory are: accidentally piercing the gel while loading, not loading enough of sample into
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