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

cause it takes the subjectivity away from the determinations. The software allows the user to isolate the range of fragment lengths necessary for proper hybridization onto microarrays, and gives the user the percent of the total area that the range covers. These tools are utilized to ensure that the samples have been fully fragmented to the proper size range. If the samples do not have a high enough percentage of total area in the proper size range then they are heated for an additional amount of time to allow adequate fragmentation. Examples of varying levels of fragmentation are shown below (Figures 11-15).


The mRNA Smear Nano assay is clearly a useful means for examining the fragmented cRNA samples. In a MOPS gel image it is not always easy to tell whether or not a sample is fragmented to sufficient lengths necessary for hybridization. Samples that may need to be heated longer may not be recognized, and their hybridization onto the arrays may be affected. By using the Agilent 2100 bioanalyzer it is easy to see which samples are not fully fragmented.


Conclusion

The Agilent 2100 bioanalyzer and the RNA 6000 LabChip Kit were used to analyze the quality of the total RNA and fragmented cRNA. The Eukaryote Total RNA Nano and mRNA Smear Nano assay gave clear, distinct results. It is easy to draw conclusions from the electropherograms created using the Agilent software. The whole Agilent process is less time consuming, less subjective, more reliable, and is suitable for use in a high throughput environment. Money could also be saved on reagents, microarrays and samples because more concrete data is being generated with the Agilent
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