MicroRNA Array Services  Exiqon’s ISO 9001:2000 certified microRNA profiling service covers everything from an initial consultation to the final data analysis. The service is carried out with automated hybridization stations in state of the art ozone-free laboratories using our latest generation of miRCURY LNA™ microRNA microarray products. Your results will be presented in an easy-to-read report within 2-4 weeks. Learn more about the different steps of the process by clicking the tabs below.
Niels M. Frandsen, Ph.D., Product Manager | |
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When you place an order with Exiqon's microRNA Profiling Services, you are assured direct communication with the scientists performing your experiments throughout the duration of the project. Each service project begins with a free consultation with an expert who has a wealth of experience in microRNA expression profiling. At this consultation, the optimal experimental design and final data analysis is discussed and agreed upon.
Preferred experimental setup
It is crucial for the success of the profiling study that the chosen experimental setup is designed for your specific needs, and we put a lot of effort into finding the optimal design. Based on the number and type of comparisons you wish to make, we will offer advice on whether to choose a common reference, universal reference or direct comparison setup.
Samples
For good results, it is very important to use high quality RNA samples. At the initial consultation we will offer advice on methods of purification and the number of biological replicas needed. If possible, it is therefore ideal if the consultation takes place before you prepare your RNA samples. Please find more details on sample preparation, sample size and sample type under the “Sample submission” section of the workflow above.
Choice of arrays
You will be given the choice between the two available types of miRCURY LNA™ microRNA Arrays (version 11.0 of our human, mouse and rat array or version 11.0 of our other species array). Our array platform is the most sensitive platform on the market. Due to the incorporation of LNA™ in the capture probes, more than 90% of our probes have a detection limit of less than 10 amol (Figure 2). This enables us to perform microRNA profiles with very low levels of total RNA input. All our capture probes are Tm-normalized to ensure uniform and high quality performance across the array. Read more about the miRCURY LNA™ microRNA Arrays
Data analysis
Our profiling service includes a data analysis summary report which is described in detail in the “Report” section of the workflow above. At the initial consultation we will discuss how the data analysis is optimized in relation to the chosen experimental setup.
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Figure 1
Workflow of a microRNA Array Services project. (Click to learn more)
Figure 2
Detection limits of miRCURY LNA™ capture probes. (Click to learn more)
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After discussing the experimental design with our scientists, you will be asked to complete the sample submission form . Technical specialists will review the information to make sure that there are no outstanding questions and will then ask you to ship your samples. Whether you wish to submit only a few or several hundreds of samples we are happy to accept your order. Please find some guidelines on sample preparation, size and type below.
Sample preparation
High quality sample preparation is probably the most important step of a microRNA profiling experiment. First of all, it is crucial to ensure that small RNAs are not lost in the extraction steps. Also, the purity of the preparation is very important for high quality data. At the initial consultation of our profiling service we will offer recommendations for suitable extraction and clean-up methods as well as RNA quality cut-off criteria.
It is important to keep in mind that with every manipulation of your RNA sample there is a risk of introducing an experimental bias. The miRCURY LNA™ array platform is not affected by the presence of mRNA and therefore we normally recommend working with total RNA. However, we can also run your experiment with samples enriched for small RNA. In this case, we kindly request you to send us at least 100ng of the corresponding total RNA per sample for quality control purposes.
Sample size
The amount of RNA needed for microRNA profiling depends on the type of experiment conducted. We can generate biologically significant results using 200-300 ng total RNA and even less if comparing samples that are very different (Figure 3). However, for optimal sensitivity we recommend using total RNA samples of 1-2 µg depending on the experiment. Half of this amount can be used as a common reference or in a dye swap experiment. If you wish to perform your profiling experiment with very small amounts of total RNA, please contact us.
Sample type
We work with total RNA from all sample types such as cell line cultures, blood, animal tissue and clinical samples. Many of our customers express interest in generating microRNA profiles from formalin-fixed paraffin-embedded (FFPE) samples. We have compared RNA quality and microRNA profiles of samples derived from FFPE and fresh frozen (FrFr) samples prepared from the same tissue (Figure 4). While RNA from FFPE samples was considerably degraded, we still observed very good correlation between microRNA profiles obtained with FFPE and FrFr samples. This suggests that microRNA is much more stabile in FFPE samples than mRNA. The high correlation is a good example of the advantages of our selective LNA™ capture probes and high stringency hybridization conditions, which make our platform robust towards interference from small mRNA degradation products.
Please contact us for advice on how to extract RNA for FFPE samples, as some methods may be unsuitable.
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Figure 3
Excellent correlation between different amounts of input RNA. (Click to learn more)
Figure 4
Good correlation between microRNA profiles from FFPE and fresh frozen samples (Click to learn more)
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After receiving your RNA samples, our specialists will assess the integrity of each sample and determine its concentration spectrophotometrically using Bioanalyzer and NanoDrop™ instruments. The results of this assessment will be made available to you on Exiqon’s secure web server. Resubmission of samples with inadequate RNA quality may be required.
For submissions of enriched RNA samples we request that you, in addition to the enriched sample, submit at least 100 ng of the corresponding total RNA, i.e., pre-enrichment sample or left over fraction, for quality control and quantitation purposes.
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Following quality control, your RNA samples will be labeled using our miRCURY LNA™ microRNA Power Labeling Kit for efficient and uniform labeling. Next, the labeled samples will then be hybridized to the miRCURY LNA™ microRNA Arrays . All hybridization and washing steps are fully automated to ensure high reproducibility (Figure 5).
We have invested heavily in our laboratory facilities to provide fast, high-throughput service. Our laboratories use Tecan HS4800™ Pro automated hybridization stations and Agilent G2505B Microarray Scanners operated in an ozone-free environment to avoid bleaching of the fluorescent labels.
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Figure 5
Our microRNA profiling service offers very high reproducibility (Click to learn more)
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When your results are ready, your data will be analyzed based on your project and individual needs. Image analyses will be performed in order to quantitate the signals of the arrays and a technical quality assessment of the data is performed based on results from synthetic spike-in control RNAs. Our experienced scientists have intimate knowledge about our array platform and a profound understanding of how to handle and interpret microRNA profiling data. This allows them to adopt the most suitable methods for normalization and statistical data analysis to the project at hand.
Delivery of report Upon completion of the microRNA Array service, you will receive an email with a link to a secure web-server from which you can download the final report and all associated files. The summary report provides a quick overview of the results along with publication-grade illustrations. The report also contains all information required for deposition of results in public gene expression databases according to the MIAME guidelines. Our microarray platforms have been deposited with the NCBI Gene Expression Omnibus (GEO) repository. This was done to facilitate MIAME compliant data submission, which is often a requirement for publication in scientific journals. Contact us for additional consultation with Exiqon scientists.
Depending on the size of your service order, we guarantee delivery of results within 2-4 weeks of receiving your samples.
A growing list of publications based on results generated from our services is a testimony to our commitment to provide the best possible service and high quality data to our customers (see “Scientific publications” in the right hand menu).
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