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miRCURY LNA™ Arrays for microRNA expression profiling  Featuring validated and T m-normalized LNA™-based capture probes, the miRCURY LNA™ arrays offer global microRNA expression profiling with unmatched specificity and sensitivity.
Carsten Alsbo, Ph.D., Product Manager Back | |
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- Broadest coverage on the market – get access to all miRBase v.14 microRNAs and our miRPlus™ sequences. A multi-species array is also available
- Excellent sensitivity and specificity – Tm-optimized capture probes for detection of ALL microRNAs, regardless of GC-content
- Start from as little as 30 ng total RNA
- Thoroughly validated LNA™-enhanced capture probes
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Sensitive microarrays with superior microRNA coverageExiqon’s microRNA arrays feature Tm-normalized LNA™-enhanced capture probes, designed for excellent specificity and sensitivity even for AT-rich microRNAs. In addition, they offer great reproducibility with 99 % correlation between arrays and a dynamic range greater than 4 orders of magnitude.
We offer a complete solution for microRNA array profiling. Use our miRCURY™ RNA Isolation Kits to prepare total RNA suitable for use with our miRCURY LNA™ microRNA Power Labeling Kits. The microarrays ship complete with buffers and spike-in microRNAs. Protocols are available for Tecan and MAUI hybridization stations as well as for manual hybridization. Furthermore, instructions for use in dual or single color experiments are also provided.
For more information on our miRCURY LNA™ Arrays, click the “Experimental data” tab above.
CoverageWe offer two different microRNA microarrays:
miRCURY LNA™ microRNA Array, 5th gen - hsa, mmu & rno The 5th generation of our array contains more than 1891 capture probes, covering all human, mouse and rat microRNAs annotated in miRBase 14.0, as well as all viral microRNAs related to these species (Table 1). In addition, this array contains capture probes for 385 new miRPlus™ human microRNAs. These are proprietary microRNAs not found in miRBase.
miRCURY LNA™ microRNA Array, v. 11.0 -Other Species
This array contains close to 2500 capture probes from species other than human, mouse and rat. It has a unique coverage of 4168 mature microRNAs from 85 species, and can be used for microRNA profiling from vertebrates, invertebrates, plants and viruses and for cross-profiling between species. Please refer to Table 1 for details.
Table 1
Coverage of miRCURY LNA™ microRNA Arrays for 115 organisms. (Click to learn more)
Content- miRCURY LNA™ microRNA Arrays are available in sets of 3, 6 or 24 pre-printed arrays or as ready-to-spot probe sets for your own printing.
- They ship complete with all array hybridization and washing solutions.
- 52 synthetic spike-in microRNAs are included with the miRCURY LNA™ microRNA Array 5th gen hsa, mmu & rno products. 10 are included in the Other species array. These are ideal for use in control experiments, normalizations and more.
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Uniform profiling of all microRNA across Tm-normalized array 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 meaning variable microRNA binding affinities, if full length probes are used (Figure 1). This is critical to an array, where a large range of microRNAs should be profiled equally at the same hybridization temperature.
This means that in order to normalize melting temperatures, the probe-target duplex having the lowest Tm, 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 Tm. 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 Tm–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 Tm-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 1, the Tm of LNA™ capture probes are increased and the Tm 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 2).
Unmatched sensitivity of validated array All capture probes have been thoroughly validated to ensure optimal performance of the miRCURY LNA™ microRNA Array. The sensitivity of the array has been assessed by empirically using synthetic microRNAs. As shown in Figure 3, more than half of the LNA™ capture probes on the array have a detection limit of ≤1 amol, while most microRNAs (93%) can be detected at levels of 10 amol or less. This enables microRNA profiling with very small amounts of total RNA.
Sample input of 30 ng total RNA is sufficient
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 4). 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.
High specificity with 1 nt discrimination 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 5).
Broad 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 6).
Get microRNA information ahead of your colleagues with miRPlus™ 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. The sequences are subjected to strict quality control to ensure that they...
- 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
The miRPlus™ sequences give scientists unique information about microRNAs not available elsewhere (Figure 7).
The first miRPlus™ capture probes appeared on the miRCURY LNA™ microRNA Array in the middle of 2006 and over the years, 714 miRPlus™ probes have been featured on various versions of the arrays. Out of these sequences, 250 are annotated in miRBase v. 14, 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.
Highest microRNA coverage on the marketWith the launch of our 5th generation human, rat and mouse array, more miRPlus™ capture probes have been added. This means that the miRCURY LNA™ microRNA Array can now detect close to 1300 human microRNAs and an additional 106 human viral microRNAs (Table 1). This is by far the highest coverage of human microRNAs available on the market.
Table 1
| 904 |
Mature human microRNAs |
| 106 |
Mature human viral microRNAs |
| 385 |
Mature miRPlus™ human microRNAs |
| 1395 |
Human microRNAs in total | Coverage of the miRCURY LNA™ microRNA Array. (Click to learn more)
Spike-in miRNA Kit v2 for data quality improvement The human, mouse and rat microRNA array includes a kit with 52 synthetic spike-in microRNAs that can be detected on the array 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 52 spike-in microRNAs in 1 µg total RNA.
In addition, the array contains capture probes for another 10 spike-in microRNAs, which can be used for further calibration or control of the profiling experiment.
Robust system with high 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 coefficient of variation (CV) values of the four replicate spots as well as excellent correlation between individual array slides (Figure 10).
Dual or single-color experiments
The production of our latest 5th generation array have been further optimized in order to support single-color experiments. Table 2 summarizes some of the advantages of using single or dual color protocols.
Table 2
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Advantages |
Disadvantages |
| Dual color |
- Lowess normalization reduces differences caused by experimental variation
- Lowess normalization reduces day-to-day variation
- Ratio data are typically more robust than absolute signals
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- With common reference: Can only be done on a limited project with known number of samples and requires double the amount of RNA.
- With universal reference: miRs expressed in samples but not in reference are measured inaccurately.
- Hy5 is sensitive to ozone and might pose problems especially in urban areas if counter measures have not been taken in the lab to ensure low ozone levels
- Requires double the amount of RNA sample than single color
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| Single color |
- Enables comparison across experiments
- Ability to add more samples to an experiment later
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- Requires extremely high lab standards and very reproducible handling of samples
- Experiments performed over a large time span are sensitive to minor lot-to-lot variations
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Validate your results with miRCURY LNA™ Universal RT microRNA PCR
Our new microRNA PCR system offers the best available combination of performance and ease-of-use on the microRNA real-time PCR market for validating your microarray results. The combination of a Universal RT reaction and LNA™-enhanced PCR primers results in unmatched sensitivity and specificity. The Ready-to-use microRNA PCR panels enable fast and easy microRNA expression profiling. (Figure 11). Identical positive controls on both platforms allows for robust cross-platform comparison of results
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Figure 1 LNA™ capture probes have a narrower Tm range than DNA probes. (Click to learn more)
Figure 2 LNA™ probes are less sensitive to variations in microRNA GC-content.(Click to learn more)
Figure 3 Detection limits of miRCURY LNA™ capture probes. (Click to learn more)
Figure 4 Excellent correlation between different amounts of input RNA. (Click to learn more)
Figure 5 LNA™ probes discriminate between single nucleotide target differences. (Click to learn more)
Figure 6
LNA™ based arrays detect microRNAs over a wide dynamic range. (Click to learn more)
Figure 7
Get access to the unique miRPlus™ microRNAs. (Click to learn more)
Figure 8 Thorough data quality assessment using the Spike-in miRNA Kits v2. (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
Excellent correlation between miRCURY LNA™ microRNA Arrays and PCR results. (Click to learn more) |
Changes in Gene Expression in Response to Starvation
 “The miRNA Profiling Services at Exiqon has performed the technical aspects of the analysis, a task which requires time and specialized knowledge. This has allowed us to focus on the quality of biological aspects of the experiment.”
Dr Tom Hamborg Nielsen, Associate Professor and group leader, and Dr. Maria Lundmark, Post Doctoral researcher, both work at the Plant Molecular Biology Laboratory at Copenhagen University, Denmark. They study how plants respond to phosphate starvation by changing their gene expression.
“Even microRNAs with a high level of similarity could be distinguished well using these arrays”
 “The results show some differentially regulated miRNAs and a nice overlap of expression regarding miRNAs encoded by a common primary transcript.”
Dr. Roman-Ulrich Müller, Zentrale Klinishe Forschung, Uniklinik Freiburg.
 “the miRCURY kit is really easy to use and we obtained good quality data” Dr Shane Murray is a plant genomics expert at the Centre for Proteomic and Genomic Research (CPGR) in Cape Town, South Africa. The CPGR is a modern world class, high throughput biology research facility that provides state-of-the-art analytical services and technical expertise in the genomics and proteomics sectors.
Bali Muralidhar is working in Dr Nick Coleman's group at the Medical Research Council Cancer Cell Unit in Cambridge, UK. The group is investigating novel approaches to cancer diagnosis. This involves two main areas: - The development of novel markers for improved screening for cervical cancer and colorectal cancer.
- The mechanisms of cervical neoplastic progression.
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"The superior detection sensitivity eliminates the need for RNA size selection”
 "More answers than questions when it comes to data analysis and interpretation."
Prof Martina Muckenthaler and Prof Matthias Hentze, University of Heidelberg and EMBL, Germany
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