MicroRNA Microarray

Figure 1. ORB’s microRNA microarray characterization services can use the cost-effective and biofluid compatible ORB miRBase 19 platform or the Affymetrix microRNA 4.0 array which provides comprehensive coverage and unique content.

ORB's microRNA profiling service combines high quality microarrays, a reproducible laboratory process, in-depth analysis services, and the best pricing in the industry. ORB scientists have optimized labeling chemistry and the hybridization process to minimize RNA input requirements. Also, ORB has developed a complete suite of reproducible protocols for isolation, quality assessment, and microarray-based microRNA analysis of RNA from biofluids. The company also has implemented standardized protocols for profiling of microRNA from formalin fixed paraffin embedded (FFPE) tissue.

ORB offers microRNA characterization using two different microarrays: ORB’s proprietary version 19 multi-species array and the Affymetrix 4.0 platform. Both arrays are optimized to examine RNA samples extracted from cellular and tissue samples, and the ORB miRBase 19 microarray can also be utilized to examine a wide variety of biofluid samples which is particularly useful for biomarker discovery investigations. The ORB microRNA microarray produces reliable data from as little as 50 nanograms (ng) of cellular RNA, whereas the Affymetrix microRNA microarray requires a minimum 130 ng of RNA per sample. The sensitivity of ORB's microRNA array system enables profiling of microRNA from challenging specimens such as isolated microvesicles, flow-sorted immune cells, and laser captured microdissected samples. Each array can measure expression levels of mature microRNAs from human, mouse, and rat samples In addition, the Affymetrix array, which is based on miRBase version 20, covers pri-microRNAs for these species and variety of other small RNA species.

ORB offers a full suite of RNA isolation services including various cell-free biofluids, PaxGene tubes, fresh-froze or FFPE-preserved tissue, and cultured cells. Complementing ORB's laboratory microRNA analysis capabilities, the company also provides flexible and comprehensive services for statistical and pathway analysis of microRNA expression data. These capabilities in combination with competitive pricing make ORB a leader in the provision of microRNA profiling services and the best solution for effective use of your research funds. For more details about ORB microRNA microarray offering please see the available platforms below.

Available Microarrays

Affymetrix GeneChip miRNA 4.0 Array (Datasheet)

Affymetrix GeneChip miRNA 4.0 microarray is an ideal choice for researchers seeking the greatest coverage of small non-coding RNA transcripts from standard input tissue or cultured cell profiling projects where cost is less important. The array contains 30,434 probe sets based on miRBase 20, providing full coverage of known mature microRNAs in over 200 species including viruses, as well as coverage of pre-miRNA in human, mouse, and rat. The array also contains 1,996 probe sets to cover additional non-coding human small RNA such as snoRNA, CDBox RNA, H/ACA Box RNA, and scaRNA. The CEL files which are generated from these arrays can be analyzed using the Affymetrix Transcriptome Console Software to examine differential expression and visualize results. For detailed information on the GeneChip miRNA 4.0 array including specific coverage information for the model organism of your choice, refer to the datasheet.

Version 19 Multispecies MicroRNA Array

ORB's version 19 multispecies microarray is the most cost-effective option to measure mature microRNAs across the industry, and due to its superior sensitivity, this array is an excellent option for the detection of low abundance mature microRNAs, especially when sample mass is limiting (e.g. 50 nanograms of tissue-derived RNA). Moreover, the ORB microRNA array is optimized for biofluids (e.g. serum and plasma) as well as FFPE tissue. This array provides full coverage of mirBASE version 19 in three species, including 2,040 human, 1,280 mouse, and 723 rat mature and minor form(*) microRNAs. (Version 21, which uses miRBase 21, is in preparation.) The array is triplicate spotted and contains 46 control probes to enable the monitoring of sensitivity, specificity, and reproducibility for every sample hybridized. This array has excellent intra-experiment reproducibility and also is backward compatible with ORB's previous microarray versions, providing the researcher with the ability to compare current data with previous studies. To learn more about the array design, production and quality control, visit the system features page. A demonstration report from an analysis of six (6) human tissue samples as well as sensitivity, reproducibility, and, specificity data are provided on the performance data page.

All ORB MicroRNA Arrays Feature:
  • Spotted in triplicate
  • 28 negative controls
  • 12 mismatch controls
  • 11 spiking controls

Comparison of ORB’s version 19 microRNA Array and the Affymetrix GeneChip miRNA 4.0 Array

ORB’s microRNA microarray options are carefully selected based on each array's unique advantages that are important to researchers. While both ORB’s proprietary v19 and the Affymetrix miRNA 4.0 arrays produce reliable and accurate results which can be utilized in biomarker discovery studies, the cost and coverage vary between these platforms. See Table I for more information about these arrays.

Table I. Comparison of performance specifications and coverage of ORB’s version 19 multispecies and Affymetrix microRNA 4.0 microarrays.
Metric ORB v19 Affymetrix 4.0
Cellular RNA input 50 ng 130 ng
Biofluid RNA input 500 pg NA
Sequence Probe Count
Sequence ORB v19 Affymetrix 4.0
Probes per probe set for mature miRNA 1 8-12
Human mature miRNA 2,040 2,578
Mouse mature miRNA 1,280 1,255
Rat mature miRNA 723 728
Human snoRNA, CDBox RNA,
H/ACA Box RNA and scaRNA
NA 1,996
Human pre-miRNA NA 2,025
Mouse pre-miRNA NA 1,225
Rat pre-miRNA NA 490
Figure 3. Identification of inflammatory bowel disease circulating microRNA markers with ORB’s proprietary microRNA array. See our Biofluid MicroRNA Microarray page for more information about this investigation of sera from patients with Crohn's disease, ulcerative colitis, and rheumatoid arthritis.

Sample Types Suitable microRNA Microarray Processing

  • Tissue biopsies
  • Cells
  • Microvesicle/ exosome
  • Whole Blood - PaxGene
  • Serum
  • Plasma
  • Cerebrospinal Fluid
  • Lymphatic Fluid
  • Bronchial Lavage
  • Ascites Fluid
  • Saliva
  • FFPE tissue

ORB provides microRNA isolation services from a wide variety of samples. Contact us about the processing of sample types which are not included in the list above. ORB is a Biosafety Level 2 (BSL-2) laboratory, and can accept samples which contain agents associated with human disease.

Table II. Starting Input Requirements and Sample Submission Checklists for ORB’s microRNA microarray services.

  Sample Fraction
Input Total RNA (ng) Total Fluid (ml) Microvesicle/
exosome (ml)
Cells Tissues (mg)
Standard 3000 1 4 3x10^6 10
Low 50 0.2 1 5x10^4 1.5

Click starting input requirements provided in Table II for corresponding sample submission checklist. When shipping, enclose a completed sample submission checklist in a separate dry compartment with the sample shipment. Also send a digital file version of the sample submission checklist to array@oceanridgebio.com and provide notification of the sample shipment to by calling 754-600-5128 on the day samples are shipped.

MicroRNA Profiling Service Pricing

Table III. List Pricing for service using ORB's version 9.0 multispecies microRNA or Affymetrix miRNA. 4.0 array.
  Price Per Sample*
Number of Samples ORB v19 Affymetrix 4.0
6-11 $521 $696
12-23 $470 $645
24-47 $421 $596

*Download our price sheet for the latest volume discounts. Standard service includes evaluation of RNA sample quality, DNase digestion, purification of low molecular weight RNA, labeling, hybridization, quality control report, and a full data analysis package. All materials are included and no extra charges apply.

MicroRNA Microarrays Data Analysis Packages

Standard Bioinformatic Services
  • Full data quality control report
  • Excel tables containing the results of multi-factor ANOVA and post-hoc Tukey tests, fold-changes, and full annotation information. Both log2– and untransformed versions of the data are provided.
  • Hierarchical clustering
  • Principal component analysis
  • PowerPoint summary containing a description of laboratory and data processing steps as well as key results of the study.
Additional Services
  • MicroRNA target pathway examination
  • mRNA microarray data correlation
  • Predictive modeling

Related Services

As mentioned above, ORB’s microRNA microarray service is optimized for many biofluids, including serum and plasma, and can be applied to either the total or microvesicle-associated fraction of these samples. In addition, ORB can provide analysis of microRNA and other small RNAs in whole biofluids (or exosomes derived from biofluid) by RNA sequencing. ORB also performs methylation analysis and oncogene sequencing using cell-free DNA isolated from serum and plasma, and offers multiplex protein profiling using these same sample types. Click on the biofluids icon link below for more information.

Major applications for profiling of microRNA and other macromolecules in biofluids are biomarker discovery and companion diagnostics; pages covering these applications (linked below) are intended to provide a broad overview of those fields along with descriptions of ORB's specific services which may be applicable. As part of ORB's services for biomarker discovery projects, the company can provide validation of expression changes observed for specific microRNA candidates using ABI Taqman real-time PCR assays. ORB also provides support to clients when additional information is required for FDA filings, manuscript preparation, and patent applications, generally at no extra charge.

As mentioned above, tissue preserved by the formalin fixation and paraffin embedding (FFPE) process can  be used as a source of RNA for microRNA profiling by microarray. FFPE samples are even more closely associated with biomarker discovery than biofluids in the pharmaceutical industry because it is common practice to collect and archive FFPE tissue blocks as part of many clinical trials. ORB also has the capability to characterize small RNA derived from FFPE specimens by Illumina sequencing. 

Bioinformatic services, including MicroRNA targets prediction, pathway analysis of predicted microRNA targets,  and predictive modeling round out the microRNA-related research services available to ORB clients. Please follow links below for further details on some of these related services.

Contact us to discuss the best profiling option for your microRNA study!