miRCURY LNA™ Arrays for microRNA expression profiling Featuring validated and Tm-normalized LNA™-based capture probes, the miRCURY LNA™ arrays offer global microRNA expression profiling with unmatched specificity and sensitivity.
NEW! Instructional movie on manual hybridization.
Carsten Alsbo, Ph.D., Product ManagerBack | |
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- Sensitivity - microRNA profiling possible from as low as 30 ng total RNA
- Specificity - efficient discrimination between closely related microRNA family members
- Coverage - get access to 428 unique human microRNAs (miRPlus™)
- Reproducibility - high reproducibility with 99% correlation between arrays
- Dynamic range - greater than 4 orders of magnitude
- Diversity - the most comprehensive probe set available
- Open platform - protocols available for Tecan and MAUI hybridization stations, and for manual hybridization.
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Features - Based on Tm-normalized LNA™ array capture probes, designed for maximal specificity and sensitivity.
- Includes 10 synthetic spike-in microRNAs ideal for use in control experiments, normalizations and more.
- Ships complete with all array hybridization and washing solutions.
- Designed for hybridization of total RNA. No further enrichment steps required.
- Available in sets of 3, 6 or 24 arrays or as ready-to-probe sets.
- Designed for use with our miRCURY LNA™ microRNA Power Labeling Kits
For more information on our miRCURY LNA™ Arrays, click the “Experimental data” tab above.
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Coverage We currently offer two miRCURY LNA™ microRNA Arrays:
Version 11 of our human, mouse and rat array (v. 11.0 - hsa, mmu & rno array) contains more than 1700 capture probes, covering all microRNAs annotated in miRBase 11.0, as well as all viral microRNAs, related to these species. In addition, this array contains capture probes for 428 new miRPlus™ human microRNAs. These are proprietary microRNAs not included in miRBase . However, 30 % of the currently annotated human microRNAs were available in our miRPlus™ range of products prior to publication in miRBase. It is therefore likely that many of our current miRPlus™ sequences will be added to miRBase in the future.
The 9.2 all species array contains more than 2000 capture probes, making it possible to profile miRBase 9.2 microRNAs from any organism – vertebrate, invertebrate, plant and virus – and to cross profile between species. Ready-to-spot probe sets are available for both types of arrays. Contact us for more information.
Click here to see the coverage of our miRCURY LNA™ microRNA Arrays to microRNAs from all species annotated in miRBase v. 13.0.
Download of GAL-files for miRCURY LNA™ arrays
Download of microplate layout files for miRCURY LNA™ array ready-to-spot probe sets
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Table 1 
Exiqon miRCURY™ products - Coverage of miRBase 13.0. (Click to learn more.) |
Contents |
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miRPlus™ - proprietary human microRNAs In addition to the microRNAs annotated in miRBase, our miRCURY LNA™ microRNA Arrays contain miRPlus™ capture probes. These probes target proprietary microRNAs that have been identified by Exiqon using cloning and sequencing of human normal and diseased tissue. Before being added to our miRCURY LNA™ microRNA Arrays, the sequences are subjected to strict quality control to ensure that they...
- are are found in several instances
- are found in the human genome
- are truly different from annotated microRNAs
- have sequence structures like those of annotated microRNAs
- have precursor sequences that can form stem-loop structures
- are expressed in a tissue specific manner, like annotated microRNAs
Once they have been added to the arrays, the miRPlus™ sequences give scientists unique information about microRNAs not available elsewhere (Figure 1). The first miRPlus™ capture probes appeared on the miRCURY LNA™ microRNA Array in the middle of 2006 and over the years, 709 miRPlus™ probes have been featured on various versions of the arrays. Out of these sequences, 243 are annotated in miRBase v. 13, which means that almost 30% of the currently annotated human microRNAs were available on our arrays at some point before they were included in miRBase. This clearly demonstrates the high quality of our miRPlus™ microRNAs and represents yet another benefit for scientists using our miRCURY LNA™ microRNA Arrays.
428 new human miRPlus™ capture probes On version 11 of our human, rat and mouse array, 428 new miRPlus™ capture probes have been introduced. This means that the miRCURY LNA™ microRNA Array can now detect close to 1300 human microRNAs and an additional 80 human viral microRNAs (Table 1). This is by far the highest coverage of human microRNAs available on the market.
Table 1
| 854 |
Mature human microRNAs |
| 80 |
Mature human viral microRNAs |
| 428 |
Mature miRPlus™ human microRNAs | Coverage of the miRCURY LNA™ microRNA Array. (Click to learn more)
The miRPlus™ sequences are normally submitted to miRBase within 6-12 months; however, researches can get access to the sequences by signing a non-disclosure agreement.
Tm-normalized LNA™ capture probes Since microarray slides are hybridized and washed at set temperatures, it is important that the duplexes formed between the probes and their targets have similar melting temperatures. In this respect, microRNAs represent a special challenge. First, their short lengths mean that probes targeting these sequences also need to be short. Second, the variations in GC content (between 25-90% in human) of microRNAs will result in highly variable melting temperatures, if full length probes are used (Figure 1).
This means that in order to normalize melting temperatures, the probe-target duplex having the lowest T m, i.e. the most AT-rich, must be used as reference. As the GC-content of the microRNAs increase, the targeting probes will need to be shorter to maintain the T m. For microRNAs with high GC-content the probes will need to be as short as 8-9 nucleotides, at which point the specificity of the array will suffer. This means that T m–normalization of pure DNA capture probes is not possible without compromising specificity and sensitivity of some of the probes.
This paradox is solved by incorporation of LNA™ in the capture probes of the miRCURY LNA™ microRNA Arrays. By adjusting the LNA™ nucleoside content as well as the length of the probes, the capture probes have been T m-normalized to ensure that all microRNA targets hybridize to the array with equal affinity under high-stringency hybridization conditions. The LNA™ capture probes have been designed according to empirically derived algorithms to maximize the affinity and specificity for their microRNA target. As shown in Figure 2, the T m of LNA™ capture probes are increased and the T m range is narrowed significantly compared to DNA probes. This makes miRCURY LNA™ microRNA Arrays superior to DNA-based arrays, especially when it comes to the detection of AT-rich microRNAs (Figure 3).
Sensitivity The sensitivity of miRCURY LNA™ microRNA Arrays have been assessed by empirically testing 705 human microRNA capture probes using synthetic microRNAs. As shown in Figure 4, more than 90% of the LNA™ capture probes on the array have a detection limit of ≤10 amol, enabling microRNA profiling with very small amounts of total RNA.
Sample input
The high sensitivity of miRCURY LNA™ microRNA Arrays means that reliable results can be obtained from as little as 30 ng of total RNA (Figure 5). Because of the high specificity of miRCURY LNA™ microRNA Arrays, you can use as much sample as you would like and still get specific results. This is important if you would like to study microRNAs expressed at low levels.
Specificity miRCURY LNA™ microRNA Arrays are highly specific for their microRNA targets. The combination of T m -normalized LNA™ capture probes and hybridization conditions optimized for high stringency binding, raises the specificity of the capture probes. The optimized LNA™ capture probe design provides superior distinction between closely related microRNAs and will, in most cases, be able to specifically distinguish between microRNAs that differ by only one nucleotide (Figure 6).
Dynamic range
miRCURY LNA™ microRNA Arrays offer superior dynamic range over more than 4 orders of magnitude, ensuring that microRNAs with high and low expression levels will be detected well within the linear detection range (Figure 7).
Spike-in microRNAs for data quality improvement
All miRCURY LNA™ microRNA Array products include 10 synthetic spike-in microRNAs that can be detected on the arrays by specifically designed capture probes. When the spike-in microRNAs are added to the labeling reactions before a dual-color array hybridization, the signals from the spike-in capture probes can be used:
- as a control for the labeling reaction and hybridization
- to calibrate/adjust scanner settings between channels
- as a control for the data normalization procedure
- to estimate the variance of replicated measurements within arrays
- to assess the technical variability between different parts of the array
Figure 8 illustrates the position of the 10 spike-in microRNAs in 1 µg total RNA.
Reproducibility
The miRCURY LNA™ Array features very high reproducibility through an optimized manufacturing process that ensures high quality uniform spots (Figure 9). This results in very low CV values of the four replicate spots as well as excellent inter-slide correlation (Figure 10).
Cross-platform correlation
Data obtained from the miRCURY LNA™ microRNA Array displays excellent cross-platform correlation with data obtained using other profiling technologies. An example of such correlation is demonstrated in Figure 11. A comparison was made between miRCURY LNA™ microRNA Array data and published profiling data of placenta, ovary and liver tissue using small RNA cloning (Landegraf et al., 2007) or real-time PCR (Liang et al., 2007).
The RNA used for these studies were from different sources and were, therefore, subjected to significant differences with respect to variations between donors, tissue fractions and sample processing procedures. Moreover, the cloning data from some of the less abundant microRNAs constituted only 15 counts in total from the three different tissues, resulting in some “stochastic noise”. Nevertheless, the hierarchical cluster analysis showed excellent correlation between the three different techniques, resulting in tight tissue clustering independent of platform. |
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Figure 1
Get access to the unique miRPlus™ microRNAs. (Click to learn more)
Figure 2 LNA™ capture probes have a narrower T m range than DNA probes. (Click to learn more)
Figure 3 LNA™ probes are less sensitive to variations in microRNA GC-content.(Click to learn more)
Figure 4 Detection limits of miRCURY LNA™ capture probes. (Click to learn more)
Figure 5 Excellent correlation between different amounts of input RNA. (Click to learn more)
Figure 6 LNA™ probes discriminate between single nucleotide target differences. (Click to learn more)
Figure 7
LNA™ based arrays detect microRNAs over a wide dynamic range. (Click to learn more)
Figure 8 Data quality is easily assessed using our spike-in microRNA kit. (Click to learn more)
Figure 9 Spot morphology from a miRCURY LNA™ microRNA Array. (Click to learn more)
Figure 10
LNA™ based arrays generate highly reproducible results. (Click to learn more)
Figure 11
miRCURY LNA™ microRNA Arrays generate excellent cross-platform results. (Click to learn more) |
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