Reagent Kits

AATI's capillary electrophoresis instruments utilize specially designed reagent kits to analyze diverse nucleic acid samples, from small RNA to genomic DNA, and NGS library quality control.

Reagent Kit Box

Standard Sensitivity RNA Analysis Kit (15 nt)

Standard Sensitivity RNA Analysis Kit (15 nt)
500 Sample Standard Sensitivity RNA Analysis Kit (15 nt)

The Standard Sensitivity RNA Analysis Kit (15 nt) is used for the automated assessment of the quality of high concentration RNA samples. The efficient analysis of RNA is crucial to many applications, including next-generation sequencing technologies; qPCR, microarray analysis, and Northern blot analysis. To further enhance the ease of sample analysis post-electrophoresis, PROSize® 2.0 calculates the RNA Quality Number (RQN), providing a quantitative sample quality metric for downstream applications. With a quantitative measure of RNA quality and high-throughput capability, this kit is ideal for most RNA analysis applications.

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Components

Components 500 Sample Kit 1,000 Sample Kit
RNA Separation Gel 240 mL (DNF-265-0240) 500 mL (DNF-265-0500)
Intercalating Dye 30 µL (DNF-600-U030) 30 µL x 2 (DNF-600-U030)
5X 930 dsDNA Inlet Buffer 125 mL (DNF-355-0125) 300 mL (DNF-355-0300)
5X Capillary Conditioning Solution 50 mL (DNF-475-0050) 100 mL (DNF-475-0100)
SS RNA Diluent Marker (15 nt) 4 mL x 3 (DNF-369-0004) 4 mL x 6 (DNF-369-0004)
SS RNA Ladder 20 µL x 5 (DNF-382-U020) 20 µL x 10 (DNF-382-U020)
0.25X TE Rinse Buffer 125 mL (DNF-497-0125) 125 mL (DNF-497-0125)
BF-25 Blank Solution 8 mL (DNF-300-0008) 8 mL (DNF-300-0008)

Specifications

Specifications Description
Sample Volume Required 2 µL
Diluent Marker Volume Required 22 µL
Sizing Range 200 nt – 6,000 nt
Sizing Accuracy ± 5%
Sizing Precision 5% CV
Limit of Detection (S/N > 3) 5 ng/µL
Qualitative Range (per smear) 5 ng/µL - 500 ng/µL
Quantitative Range (per smear) 25 ng/µL - 500 ng/µL
Quantification Accuracy ± 20%
Quantification Precision 10% CV
Total Electrophoresis Run Time 31 min (Ultra-Short Array, 22-47); 40 minutes (Short Array, 33-55); 70 minutes (Long Array, 55-80)

Examples

The efficient and accurate analysis of RNA samples is enabled by the use of a high quality RNA ladder. In the electropherogram below, a typical separation of the Standard Sensitivity RNA Ladder is depicted. The reproducibility of the Standard Sensitivity RNA Ladder ensures the quality analysis of total RNA samples.

Figure 1
Figure 1. A typical separation of the Standard Sensitivity RNA Ladder (DNF-382) performed on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the Standard Sensitivity RNA Analysis Kit (DNF-471).

As shown in Figure 2, a total RNA separation, as viewed via an electropherogram, has three elements: the small RNA region, the small rRNA subunit peak, and the large rRNA subunit peak. For ease of viewing, the large rRNA subunit peak is highlighted purple in PROSize®, while the small rRNA subunit peak is highlighted pink. The size of the small and large rRNA subunits varies at all levels of biological hierarchy, from Domain to Species. As such, the sizes of the small and large rRNA subunits shown in the RNA Property Summary are the most common sizes for prokaryotic, eukaryotic, and plant rRNA. The RQN provides a quantitative measure of total RNA quality. An RQN of >7 indicates the sample is ideal for downstream applications including NGS.

Figure 2
Figure 2. Two separations of high quality total RNA extracted from yeast. The separation was performed using the SS RNA Analysis Kit on a Fragment Analyzer equipped with a Short Capillary Array (33-55). Each separation has three elements used in the calculation of RQN: the small RNA region, the small rRNA subunit, and the large rRNA subunit.

Poor quality total RNA is readily identified by this kit as shown in Figure 3. The top panel depicts a total RNA sample with an RQN of 6.2. Sequencing of a sample such as this could result in decreased read counts and poor quality sequencing results overall. The bottom panel depicts a completely degraded total RNA sample not suitable for sequencing. As RNA quality decreases, the quality of sequencing results declines.

Figure 3
Figure 3. Two separations of low quality total RNA. The separations were performed using the Standard Sensitivity RNA Analysis Kit (15 nt) on a Fragment Analyzer equipped with a Short Capillary Array (33-55). The top panel shows a total RNA sample from rice root that falls below the minimum RQN quality threshold of 7. The bottom panel shows a completely degraded total RNA sample from yeast.

Accurate quantification is important to the assessment of sample quality. The Standard Sensitivity RNA Analysis Kit (DNF-471) provides equivalent quantification of RNA compared to common methods of fluorometric quantification. A one to one linear relationship is observed (Figure 4) between concentrations calculated by a fluorometric instrument and the Fragment Analyzer for the same samples.

Figure 4
Figure 4. Concentrations measured by a fluorometric instrument were plotted against the concentrations measured by the Fragment Analyzer for the same total RNA samples. The observed one to one linear relationship supports the equivalency of quantification between the two instruments.
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