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miRCURY LNA™ microRNA Arrays

Ina K. Dahlsveen, Product Manager Featuring validated and Tm-normalized LNA™-based capture probes, the miRCURY LNA™ microarrays offer global microRNA expression profiling with unmatched specificity and sensitivity.

Ina K. Dahlsveen, Ph.D., Product Manager Back

How to set up a biomarker discovery screen

Learn how you can set up a comprehensive, sensitive, and rapid biomarker screening using the miRCURY LNA™ microRNA Array system. This application note describes how to perform a preliminary screen including validation of candidate microRNA biomarkers for thyroid cancer. 

Read the application note. 

  • Truly global microRNA profiling – 3100 capture probes cover human, mouse and rat microRNAs in miRBase v. 19.0
  • Tm-optimized for robust detection of ALL microRNAs, regardless of GC-content
  • Validated LNA™-enhanced capture probes for increased sensitivity and specificity
  • Excellent sensitivity - microRNA profiling starting from 30ng total RNA
  • Efficient discrimination of closely related microRNA family members
  • Leading-edge data analysis software customized to Exiqon arrays available

Sensitive microarrays with superior microRNA coverage

Exiqon’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 5 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 Hi-Power Labeling Kits. Exiqon's 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.


Coverage


miRCURY LNA™ microRNA Array, 7th gen - hsa, mmu & rno The 7th generation of our array contains 3100 capture probes, covering human, mouse and rat microRNAs annotated in miRBase 19.0, as well as viral microRNAs related to these species (Table 1). In addition, this array contains capture probes for 25 miRPlus™ human microRNAs. These are proprietary microRNAs not found in miRBase.



Table 1
Coverage of miRCURY LNA™ microRNA Arrays for 193 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 7th gen products. These are ideal for use in control experiments, normalizations and more.

Uniform profiling of all microRNA across Tm-normalized array

MicroRNA profiling is especially challenging due to the short length and variation in GC-content of these sequences. By using LNA™-enhanced capture probes, miRCURY LNA™ microRNA Arrays solve the problem of detecting ALL microRNAs with high uniform affinity, including those that are AT-rich. This results in arrays that are extremely sensitive and specific.

Figure 1 explains in more detail how Tm-normalization of the miRCURY LNA™ microRNA Array improves microRNA profiling with a higher binding affinity. Figure 2 explains how the LNA™-enhanced microRNA capture probes display superior sensitivity compared to conventional DNA-based arrays and how this enables true detection of all microRNAs even those low in GC-content.


Unmatched sensitivity of validated array

Exiqon’s miRCURY LNA™ Hi-Power microRNA Labeling Kit offers almost double signal-to-noise ratios compared to our standard labeling kit. This means that microRNAs that were previously just below the level of detection, can now be readily detected. More microRNAs can be detected from the same amount of input RNA (Figure 4). Furthermore, the same number of microRNAs can be detected with half the amount of RNA when using the Hi-Power kit (Figure 5).

ALL capture probes of the miRCURY LNA™ microRNA Arrays have been strictly selected and thoroughly validated. In addition, the arrays have been assessed empirically using synthetic microRNAs to ensure optimal performance and sensitivity for all microRNAs. This means that results obtained using these arrays can be trusted to reflect the true microRNA expression profiles in the samples.


Analysis starting from 30 ng total RNA

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 6). Because of the high specificity of the platform, the sample size can be scaled up without compromising the quality of the data. This is especially important when studying microRNAs expressed at low levels.


High specificity with single nucleotide 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 microRNA family members (Figure 7).


Broad dynamic range

miRCURY LNA™ microRNA Arrays offer superior dynamic range over more than 5 orders of magnitude, ensuring that microRNAs with high and low expression levels will be detected well within the linear detection range (Figure 8).

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 the human genome
  • are truly different from annotated microRNAs
  • have sequence structures similar to those of annotated microRNAs
  • have precursor sequences that can form stem-loop structures
  • are expressed in a tissue specific manner, as annotated microRNAs
  • have been found in multiple, independent studies, by up to 6 different research groups

The miRPlus™ sequences give scientists unique information about microRNAs not available elsewhere.


The first miRPlus™ capture probes appeared on the miRCURY LNA™ microRNA Array in the middle of 2006 and over the years, several hundred of the miRPlus™ probes that have been featured on various versions of the arrays have now been annotated 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 market

With the launch of our 7th generation human, rat and mouse array, more miRPlus™ capture probes have been added. This means that the miRCURY LNA™ microRNA Array can now detect over 1,900 human microRNAs and an additional 146 human viral microRNAs (Table 1). This is by far the highest coverage of human microRNAs available on the market.

Table 1

Organism Mature microRNAs Viral microRNAs miRPlus™
Human 1,896 146 25
Mouse 1,141 57 25
Rat 679 0 25
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 9 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 exceptionally high reproducibility

The miRCURY LNA™ Array features very high reproducibility through an optimized manufacturing process that ensures high quality uniform spots. 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 11). When used together with Exiqon's RNA labeling kits and following proper laboratory standards, median CV ≤ 10% can be obtained. Typically, Exiqon obtains median CV values of 2-4% even between different batches of the array. This allows researchers to use the array for single color experiments saving valuable sample and safely compare experiments performed at different times and over longer periods of time.


Dual or single-color experiments

The production of our latest generations of arrays has been further optimized in order to support single-color experiments. Table 2 summarizes some of the advantages of using single or dual color protocols. See our tech note on single color microarray analysis for more information.

Table 2
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
  • 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
Single color
  • Enables comparison across experiments
  • Ability to add more samples to an experiment later
  • 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


Validate your results with miRCURY LNA™ Universal RT microRNA PCR

Our qPCR system offers the best available combination of performance and ease-of-use on the microRNA qPCR market and is the ideal solution 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
  Figure 1 Tm-normalized LNA™ capture probes.

LNA™ capture probes have a narrower Tm range than DNA probes. (Click to learn more)


Figure 2 LNA™-based arrays are superior to DNA-based arrays at detecting microRNA

Unlike DNA-based microarrays, LNA™-enhanced arrays can detect all microRNAs.(Click to learn more)


Figure 3 Drastically improved sensitivity

Over 80% of microRNAs are detected at 1 amol. (Click to learn more)

Figure 4
Detect substantially more microRNAs. (Click to learn more)


Figure 5
Detect the same number of microRNAs using half the RNA input. (Click to learn more)

Figure 6 Excellent correlation
Excellent correlation between different amounts of input RNA. (Click to learn more)


Figure 7 Single mismatch discrimination

Discriminate between closely related microRNA families. (Click to learn more)


Figure 8 Superior dynamic range.
LNA™ based arrays detect microRNAs over a wide dynamic range. (Click to learn more)

Figure 9 Easy assessment of data quality. Thorough data quality assessment using the Spike-in miRNA Kits v2. (Click to learn more)

Figure 10
LNA™ based arrays generate highly reproducible results. (Click to learn more)


Figure 11 Excellent cross-platform correlation
Excellent correlation between miRCURY LNA™ microRNA Arrays and PCR results. (Click to learn more)

MicroRNA and diabetes

Tom Hamborg “We found that Exiqon's LNA™ microRNA microarrays were versatile and easy to use"

Himawan Harryanto at the University of Adelaide, Australia, studies the effect of fetal growth restriction on the development of diabetes in adult life. He has used Exiqon's microRNA microarray system to profile microRNAs in the pancreas.


Changes in Gene Expression in Response to Starvation

Tom Hamborg “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”

Dr. Roman-Ulrich Müller “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.


Shane Murray “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:
  1. The development of novel markers for improved screening for cervical cancer and colorectal cancer.
  2. The mechanisms of cervical neoplastic progression.
Read full story...


"The superior detection sensitivity eliminates the need for RNA size selection”


Martina Muckenthaler and Prof Matthias Hentze "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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