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microRNA and Small RNA Sequencing Service

Send us your samples and let our Next Generation Sequencing (NGS) experts perform your NGS analysis in state-of-the-art automated laboratories with rigorous quality control and fast turn-around times and superior data analysis and interpretation. Exiqon offers a complete sequencing service including RNA isolation, library preparation, sequencing, data analysis and biological interpretation of the results in a comprehensive and easy-to-read format.

Exiqon microRNA and Small RNA NGS Services

  • Complete sample-to-answer solution covers everything from initial consultation to thorough data analysis and interpretation
  • Provide the sample, and we will take care of RNA isolation, library preparation, sequencing, data analysis and reporting
  • Close consultation with Exiqon’s RNA and NGS experts throughout the process
  • > 9 years’ experience with microRNA profiling services
  • Sequence from as little as 100 ng total RNA
  • Rigorous quality control in all steps of the workflow
  • Fast turn-around times - delivery of the final report within 4-6 weeks
  • Combine with downstream validation by market-leading LNA™-enhanced qPCR platform

A sample-to-answer solution for NGS Service

Our microRNA and small RNA NGS service includes every step in the process: initial consultation with our microRNA and small RNA experts, RNA isolation, RNA QC, library preparation and QC, sequencing and QC, data analysis and reporting. All analyses are performed by PhD-level scientists who will ensure that you get the best service throughout the project.

A comparison of the microRNA and small RNA Sequencing Services is shown in Table 1. Libraries are size selected to maximize the number of relevant reads. You can choose to sequence either microRNAs (15-30 nt) or small RNAs (30 – 200 nt).

Table 1. A comparison of the microRNA and small RNA Sequencing Services A comparison of the microRNA and small RNA Sequencing Services

Exiqon Services provide outstanding data analysis, interpretation and visualization. Our superior bioinformatics pipeline is based on solid biological expertise in microRNA and small RNA research.

Data and results from your microRNA profiling project will be delivered in an easy-to-read report with publication grade illustrations including a data analysis files. The complete encrypted raw data can be supplied. Every project concludes with a scientific follow-up discussion with our NGS experts, to answer any questions you may have about your results.

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

microRNA sequencing

microRNA sequencing provides a comprehensive analysis of all microRNAs in the sample. Library size selection (15 – 30 nt) maximizes the number of microRNA reads. Our service includes novel microRNA discovery as well as isomiR counts, enabling you to see precisely which microRNA sequences are expressed in your samples.

microRNA sequencing is offered for 19 different standard species and a variety of custom species upon request.

Small RNA sequencing

Small RNA Sequencing provides a comprehensive analysis of all RNA species in the size range 30 – 200 nt which can include pre-microRNAs, tRNAs and snRNAs, snoRNAs and other small RNA molecules. The size range of the library can also be customized according to your particular requirements.

Contact us for more information
Exiqon mRNA and Whole Transcriptome RNA NGS Services

Figure 1 Overview of the NGS small RNA services workflow
Overview of the NGS small RNA services workflow. (Click to learn more)

1. Consultation

When you engage in a Sequencing 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 an RNA 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. Sample submission

High quality samples are important for accurate RNA sequencing. You can take advantage of our expertise and submit your samples to our RNA isolation service. Recommended sample input is 260 ng total RNA, but we get high quality results with as little as 100 ng total RNA plus 60 ng for RNA QC. We also accept samples with low RNA content, such as biofluid samples (see Biofluids microRNA Sequencing) and exosome samples (see Exosomes microRNA Sequencing). We accept samples from 19 different standard species and custom species upon request.

At the initial consultation, we offer recommendations on sample collection and handling, and on suitable extraction and clean-up methods for other samples if you wish to perform the RNA isolation yourself.

3. Sample preparation

At Exiqon Services we also offer to isolate RNA from your samples for sequencing. We perform high quality RNA isolation from a range of sample types including cells, tissues, FFPE sections, biofluids, and exosomes.

4. 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 RNA-QC results prior to the sequencing.

5. Library preparation

Following quality control, we generate libraries and select size using an automated gel cutter allowing customized size selection. The size range is tailored to maximize the number of relevant reads: 15 – 30 nt for microRNA sequencing, and 30 – 200 nt for small RNA sequencing. Library QC performed using the Bioanalyzer DNA 2100 chip.

6. Sequencing

Exiqon Services offers three types of microRNA and small RNA sequencing using the Illumina platform:
  • microRNA sequencing including microRNA discovery
  • Biofluids microRNA sequencing including microRNA discovery (learn more)
  • Exosomes microRNA sequencing including microRNA discovery (learn more)
  • small RNA sequencing
Sequencing is performed using Illumina instruments, 1x 50bp reads, 7.5M reads per sample.

7. Analysis & interpretation

Comprehensive data analysis including statistical analysis:
  • QC of raw data
  • Mapping sequences to the appropriate reference genome
  • QC of mapped data
  • For microRNA sequencing projects, microRNAs are mapped to miRBase and predicted novel microRNAs identified
  • For microRNA sequencing projects, isomiR counts can be reported
  • Differential expression analysis to identify known and novel microRNAs that are differentially expressed between your sample groups (. Statistical analysis is performed, provided there are a sufficient number of samples per group
  • Unsupervised analysis: Principal Component Analysis (PCA plot) and heatmap
  • Supervised analysis: For each specific group comparison we generate a Volcano plot to display microRNAs which are differentially expressed between the groups, list differentially expressed microRNAs as well as identify statistically significant signals
  • Biological interpretation through use of Exiqon’s knowledgebase (miRSearch) to identify validated and predicted target genes, and microRNAs sharing target genes
  • Gene Ontology (GO) enrichment analysis is performed to identify GO terms that are over-represented within the predicted and validated target genes of the microRNAs that are differentially expressed. This gives a picture of the impact of the experiment on biological pathways and processes
In connection with large service projects we also offer extensive customized bioinformatics analysis.

8. Report and final consultation

The final report is delivered as link to our secure webserver and contains:
  • An easy-to-read data report as pdf 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
  • Data analysis file which is sufficient for publication, or performing your own analysis of the data if needed
  • The complete encrypted raw data can be provided on USB3-stick at extra charge
  • Expected turnaround time: 4-6 weeks from samples passing QC at Exiqon Services
The project concludes with a scientific follow-up discussion to answer any questions you may have about your report and discuss the significance of your results and next steps. Exiqon scientists can also help you design appropriate LNA™ qPCR assays to validate your NGS data (including any novel microRNAs identified), or LNA™ tools to study the function of the candidate microRNAs of interest identified in the study.

Contact us for more information
Figure 1 Overview of the NGS small RNA services workflow
Overview of the NGS small RNA services workflow. (Click to learn more)

Comprehensive report including biological interpretation

Based on our extensive microRNA and bioinformatics expertise we have developed a unique pipeline for collecting, analyzing and visualizing NGS results.

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

Download a report example

The experimental and bioinformatics pipelines are closely integrated, enabling us to provide powerful data analysis and a final report tailored to your specifications. In addition to standard NGS data analysis, the report includes:
  • For microRNA sequencing projects, microRNAs are identified including predicted novel microRNAs
  • For microRNA sequencing projects, isomiR counts can be reported
  • Differential expression analysis to identify known and novel microRNAs that are differentially expressed between your sample groups (unlimited number of group comparisons). Statistical analysis is performed, provided there are a sufficient number of samples per group
  • Unsupervised analysis: Principal Component Analysis (PCA plot) and heatmap
  • Supervised analysis: For each specific group comparison we generate a Volcano plot to display microRNAs which are differentially expressed between the groups, list differentially expressed microRNAs as well as identify statistically significant signals
  • Biological interpretation through use of Exiqon’s knowledgebase (miRSearch) to identify validated and predicted target genes, and microRNAs sharing target genes
  • Gene Ontology (GO) enrichment analysis is performed to identify GO terms that are over-represented within the predicted and validated target genes of the microRNAs that are differentially expressed. This gives a picture of the impact of the experiment on biological pathways and processes
In connection with large service projects we also offer fully extensive customized bioinformatics analysis.

After you have received your report, we arrange a scientific follow-up discussion to answer any questions you may have about your report and discuss the significance of your results and next steps. Exiqon scientists can also help you design appropriate LNA™ qPCR assays to validate your NGS data (including any novel microRNAs identified), or LNA™ tools to study the function of the candidate microRNAs of interest identified in the study.

Contact us to discuss your project.
Louise Brogaard

microRNAs in influenza


"Exiqon is very easy and professional to work with. I was continuously kept informed of the project progress and Exiqon provided excellent follow-up support upon data delivery. They offered a great deal of flexibility.... Exiqon delivers mapped and quantified results in a report that is comprehensible for anyone."

Louise Brogaard's work focuses on the innate immune system, the first line of defense against invading microorganisms. She and her colleagues at the Technical University of Denmark use RNA sequencing to identify microRNAs involved in the response to H1N2 influenza in pigs.

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