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How it Works: Reproducible RNA Characterization and Quality Control

As with many laboratory applications, RNA QC procedures can be streamlined through automation.

by Lab901
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Problem: Many genomic techniques such as microarray and qRT-PCR analysis require the use of high-quality, intact RNA to ensure that reproducible and meaningful data are generated. Traditional RNA quality control (QC) methods have employed agarose or capillary gel electrophoresis to measure RNA degradation. This process, however, can be quite time consuming, leading to inefficiencies within the lab. When performed using capillary electrophoresis, the micro fabricated chips commonly require priming with gel, gel staining solutions and vortexing prior to the initiation of sample migration. The experimental set-up is therefore lengthy, occupying a considerable amount of a researcher’s time. The chips are often a ‘single use’ consumable, resulting in significant waste when flexibility in sample number processing is required.

Solution: As with many laboratory applications, RNA QC procedures can be streamlined through automation. Lab901’s ScreenTape® R6K system is a fully automated solution which has been specially developed for efficient and reproducible RNA characterization and quality control. This system removes time-consuming steps such as gel reagent preparation, chip priming and vortexing, to make the process faster and easier. With walk-away operation, the ScreenTape system is comprised of: the TapeStation®, which performs the liquid handling, electrophoresis and imaging steps; ScreenTape—a consumable that contains pre-cast and pre-packaged gel and buffer in 16 channels; and its bespoke GeneTools® software for the analysis of sample data. Users simply load their RNA samples and the data is generated within one minute per sample, resulting in improved throughput and efficiency.

Unlike chip-based systems, Lab901’s ScreenTape consumable can be used more than once. A single sample can be run cost-effectively each time, preserving the rest of the available channels for future experiments. This removes the need to batch samples together or throw away unused portions of the consumable, which improves the RNA QC workflow and helps laboratories reduce associated consumable costs. In addition, sample carryover issues are eliminated since ScreenTape R6K uses an individually sealed micro-gel for each sample analysis to improve reproducibility and data quality.

ScreenTape R6K automatically delivers an objective quality metric for total RNA—the ScreenTape Degradation Value (SDV)— prior to highly sensitive and time-consuming experiments such as DNA microarray and qRT-PCR. The GeneTools software will display the clearly defined small RNAs, and automatically identify and annotate the 18S RNA and 28S RNA ribosomal subunit peaks. As total RNA degrades, the less stable 28S peak rapidly disappears, followed by a more gradual deterioration of the 18S peak, while degraded material emerges between the 18S and small RNA peaks. Derived from a mathematical model that calculates a quantitative measurement of RNA degradation, the SDV therefore represents the ratio of the average degradation peak signal to the 18S peak signal. Thus, a higher SDV corresponds to a greater level of RNA degradation. A recent study carried out by LGC (the UK’s leading independent testing laboratory) compared the SDV with another integrity metric, the RNA integrity number (RIN*)1. The resulting data demonstrated that the SDV is comparable to the RIN in providing reproducible and reliable data as well as in distinguishing different levels of degradation, while differentiating more degraded RNA samples into distinct populations.

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*RIN is a software tool from Agilent Technologies

  1. Wilkes TM, Devonshire AS, Ellison SLR et al. Evaluation of a novel approach for the measurement of RNA quality. BMC Research Notes 2010; 3: 89.