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MicroRNA Array Services

Exiqon offers a comprehensive microRNA profiling service based on our miRCURY LNA™ microRNA Arrays with unrivaled accuracy and sensitivity. Let microRNA and microarray experts perform your analysis in state-of-the-art automated laboratories with rigorous quality control and fast turn-around times and advanced data analysis tailored to your research needs and budget.

Download a report example

At the end of each project, you will receive a comprehensive and easy-to-read final report. Download a report example

Exiqon microRNA Array Service at a glance

  • Covers everything from initial consultation to the final report including all raw data and detailed data analysis
  • Consultation with microRNA and array experts throughout the process
  • Profiling from as little as 200 ng total RNA
  • Fast turn-around times - delivery of the final report within 2-4 weeks of receiving your sample
  • Rigorous quality control in all steps of the analysis 
  • Normalization procedure and data analysis is optimized for each individual project

A complete microRNA array profiling service

Our microRNA array service includes every step from initial consultation, sample labeling and hybridization to full data analysis. All analyses are performed by microRNA expert scientists who will ensure that you get the best service throughout the project.

Data and results from your microRNA profiling project will be delivered in an easy-to-read report with publication grade illustrations including an Excel file with all the raw data.

The workflow of an Exiqon microRNA Aray Services project is summarized in Figure 1. Details of each step in the process are described in the following tab.

microrna profiling services workflow

1. Consultation

When you engage in a microRNA Array Service project with Exiqon, you are assured direct communication with the scientists performing your experiments throughout the duration of the project.

Each project begins with a free consultation with a microRNA expression profiling expert. Together we design an experimental setup that best satisfies your research needs and budget. Following this we will complete a detailed sample-submission form making sure that all experimental details and subsequent analysis are clearly defined and understood by both parties.

2. RNA sample submission

High quality samples are important for accurate microRNA profiling. At the initial consultation, we offer recommendations on suitable extraction and clean-up methods. Alternatively, you can take advantage of our expertise and submit your samples to our RNA isolation service.

Due to the sensitivity of our microarrays, we can perform analysis with low RNA input. We normally use between 200 - 1000ng total RNA depending on the experimental design.

3. RNA sample quality control (QC)

After receiving your RNA samples, our experts will determine the integrity and quantity of each sample using Bioanalyzer and NanoDrop™ instruments. Possible contaminations are likewise assessed for each sample. You will receive a report with the results of these analyses prior to the array profiling.

4. Labeling, hybridization and scanning

Following quality control, your RNA samples will be labeled using our new miRCURY LNA™ microRNA Hi-Power Labeling Kit for efficient and uniform labeling. Next, the labeled samples are hybridized to the miRCURY LNA™ microRNA Arrays. All hybridization and washing steps are fully automated to ensure high reproducibility.

Arrays are scanned with highly sensitive equipment and image analysis is then performed to digitalize the data. All projects include spike-in and negative control samples to determine background levels.

5. Analysis

After scanning the arrays, we perform a technical quality assessment of the data based on results from spike in controls, flagging of spots, background intensity levels and signal intensity distribution.

After normalization microarray data is assessed in multiple ways, including principle component analysis (PCA) and heat-maps with unsupervised clustering. In the biological quality assessment we check if samples group according to biology and look for any signs of experimental bias in the data set. Finally, statistical analysis of customer defined group comparisons is performed.

In connection with large service projects we also offer fully extensive customized bioinformatics analysis.

6. Report and final consultation

An easy-to-read summary report is provided containing a description of the project, assessments of sample and data quality and an overview of the results of the data analysis with publication-grade illustrations. An extensive Excel file with all raw data is also included. The final report is delivered as link to our secure webserver. See the tab “Array report” for further details on the content of the final report.

Scientific follow-up can be organized in case you have questions to your final report or wish to discuss the significance of your results further.

Great flexibility in experimental design

Our spotted microarrays allow both dual and single color experiments due to highly controlled production and strict QC-criteria. This provides great flexibility in the choice of experimental design and method of normalization.

Dual color with common reference for optimal intraslide normalization (global LOWESS), minimizing effect of sample/slide variation in labeling and hybridization efficiency.

Single color with interslide normalization (Quantile) enabling comparison of data from independent array experiments accumulating over time.

Figure 1 microrna profiling services workflow
Workflow of a microRNA Array Services project. (Click to learn more)

Figure 2 Technical reproducibility of 99%
Our microRNA profiling service offers very high reproducibility (Click to learn more)

Biomarker discovery in skin cancer

Exiqon Services has been part of numerous biomarker discovery projects and with our miRCURY LNA™ based microRNA Array system, which is superior for detecting of microRNA in clinical samples such as FFPE samples, we are uniquely positioned to assist you in all phases of biomarker discovery projects – from experimental design guidance to advanced bioinformatics.

The study Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL) published in Blood, is the result of a biomarker study between Exiqon and partners where we discover and validate a microRNA-based signature to classify skin cancer (CTCL). MicroRNA profiling for this study was performed at Exiqon Services.

Experimental design for identification of disease biomarker signatures. (Click for experimental details)

In the study miRCURY LNA™ microRNA Arrays were used to screen for promising biomarkers. Candidate biomarkers were then quantified using the miRCURY LNA™ Universal RT microRNA PCR system.

The result of the study was a skin cancer signature consisting of miR-155, miR-203, and miR-205 which distinguishes CTCL from benign disorders with a classification accuracy of 95%.

In conclusion the study shows:
  • The high diagnostic potential of microRNAs as true biomarkers
  • Demonstrate robust and reliable biomarker discovery screening using Exiqon miRCURY LNA™ microRNA Arrays
  • Demonstrate sensitive and specific validation of biomarker profiles using the Exiqon miRCURY LNA™ Universal RT microRNA PCR system
Read the paper (external link)

microRNA expression profiling from FFPE samples

A unique feature of our Array Services is our ability to provide high quality microRNA expression profiling from FFPE samples.

FFPE samples are generally characterized by poorly preserved RNA. Due to the selective nature of LNA™ capture probes and the high-stringency hybridization conditions, the miRCURY LNA™ microRNA Array platform is uniquely robust towards interference from small mRNA and rRNA degradation products typically present in FFPE samples.

Figure 1
Good correlation between microRNA profiles from FFPE and fresh frozen samples (click to learn more)

The result of your microRNA array study is presented in an easy-to-read summary report.

The report contains description of the project, assessments of sample and data quality and an overview of the results of the data analysis with publication-grade illustrations. An extensive Excel file with all raw data is also included.  The final report is delivered as link to our secure webserver.

Scientific follow-up can be organized in case you have questions to your final report or wish to discuss the significance of your results further.

The microRNA Array Profiling report consists of:
RNA sample quality control (QC) report

An easy-to-read summary report with publication-grade illustrations
  • Description of the project and workflow
  • QA/QC of sample and data
  • Plots showing the effect of normalization
  • PCA and Volcano plots
  • Heat maps based on unsupervised and supervised clustering
  • Results of statistical analysis of customer defined group comparisons.
  • Summary of results
A material and methods section
  • Ready to use for publication purposes.
Project summary Excel report with publication-grade illustrations
  • Normalized data for each individual sample
  • Expression matrices with statistical analysis according to customer specifications: T-test or ANOVA including multiple testing corrections (Benjamini-Hochberg) and indication of microRNAs that pass the statistical restriction
  • MA – and Box-plots

Figure 1
Example pages from a microRNA Array Services report.

The Sanak Lab

Identifying microRNAs involved in asthma

"It is beneficial to split a study into profiling and validation, and to benefit from the Exiqon services to conduct the experimental part that one does not have the possibility to do. We would therefore recommend this strategy to labs that are not equipped with microRNA array equipment or knowhow."

We are investigating phenotypes of bronchial asthma. As a part of this study, we use a model of air-liquid cultures of fully differentiated human bronchial epithelial cells from asthmatics and controls. The cultures are studied for response to TH2 cytokines and rhinovirus infections on the level of gene expression and production of lipid mediators. We wondered if some of these responses could be orchestrated by microRNAs.

Read full story...

Dr. Tom Hamborg

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.

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DR. Roman-Ulrich Müller

The Role of MicroRNAs in Kidney Development

"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.

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Bali Muralidhar

MicroRNA Profiling in Cervical Neoplasms

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...

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