HTG EdgeSeq miRNA Whole Transcriptome Assay 

The HTG EdgeSeq miRNA Whole Transcriptome Assay enables users to measure the expression of 2,083 human miRNA transcripts using next-generation sequencing. The HTG EdgeSeq extraction-free sample preparation chemistry is compatible with fixed tissue samples, biofluids, cell lines, and extracted RNA. The assay is powered by HTG's proprietary quantitative nuclease protection and is automated on the HTG EdgeSeq system.

Workflow & Chemistry

  • Work more efficiently by creating sequencing libraries next day 
  • Increase productivity with only 3-4 hours total hands-on time 
  • Get data faster with alignments complete in 15 to 30 minutes 
  • Simple data output enables users to get from experiment to results more efficiently

Sample Input & Compatibility

  • Generate data with > 15 µl of plasma/serum or a single 5 µm FFPE tissue section
  • No RNA extraction required across multiple sample types
Sample Type HTG EdgeSeq chemistry Technology N (Hybridization) Technology A (Microarray) Technology E (qPCR)
FFPE Tissue 1.5 to 12 mm2 of a single 5 µm section est. 6 x 10 µm tissue sections2
Extraction required
est. 8-12 x 5 µm tissue sections2
Extraction required
est. 3-4 x 5 µm tissue sections2
Extraction required
Cells > 3,000 cells 10,000 cells est. 12,500 cells2
Extraction required
est. 5,000 cells2
Extraction required
Plasma/Serum > 15 µl est. 400 µl4
Extraction required
est. 500 µl3
Extraction required
est. 250-500 µl3
Extraction required
PAXgene 500 µl est. 100 µl1
Extraction required
est. 500 µl1
Extraction required
est. 50 µl1
Extraction required
Extracted RNA > 25 ng 100 ng 50-500 ng 20 ng

*Estimates for sample inputs requiring extraction are determined based on vendor guidelines, publications and target input of purified RNA required by that technology. Sample input estimates can vary depending on the method used. 
1. PAXgene(R) Blood RNA Kit Handbook, v2. PreAnalytiX GmbH, 2009. Accessed July 2015. 
2. "RNA Content Can Vary Widely between Tissues, Cell-types, Physiological State, Etc." RNA Yields from Tissues and Cells. Web. 8 July 2015. 
3. Pinheiro, Hazel. "microRNA-Seq in Serum and Plasma." Exiqon. Webinar, 9 June 2015. Lecture. 
4. “ nCounter® miRNA Analysis in Plasma and Serum Samples." nCounter miRNA Analysis. TECH NOTE: NCounter(R) MiRNA Analysis in Plasma and Serum Samples. Nanostring Technologies. 

Performance & Applications


Consistent and reproducible performance through automation

Figure 1. To demonstrate robust chemistry and system performance, 25 ng of universal RNA was processed using the HTG EdgeSeq miRNA Whole Transcriptome Assay across 3 days. Pearson correlations of log transformed data averaged 0.99 for technical replicates (A), and day-to-day replicates (B).

Produce reliable data from precious FFPE samples

Figure 2. Matched FFPE and frozen B-cell lymphoma tissues were processed using the HTG EdgeSeq miRNA Whole Transcriptome Assay. Equivalent expression profiles are demonstrated with a Pearson correlation, r, of 0.9847


Identify or verify disease-specific biomarkers

Figure 3. miR-205 expression is a highly specific marker for squamous cell carcinoma in lung cancer (Lebanony, et al., 2009). The HTG EdgeSeq miRNA Whole Transcriptome Assay accurately measures miR205, a miR known to differentiate adeno and squamous lung carcinoma. As a control, let7a-5p expression is shown as a comparison.

Profile up to 2,083 transcripts with as little as 15 µl of plasma or serum

Figure 4. Donor plasma sample was analyzed with the HTG EdgeSeq miRNA Whole Transcriptome Assay and sequenced on the Illumina MiSeq using the v2 reagent chemistry. Pearson correlation, r, averaged at 0.9836


Catalog #


Illumina Configurations
916-001-208 HTG EdgeSeq miRNA WTA (2x8)
916-001-008 HTG EdgeSeq miRNA WTA (4x8)
916-001-224 HTG EdgeSeq miRNA WTA (1x24)
916-001-024 HTG EdgeSeq miRNA WTA (4x24)
916-001-096 HTG EdgeSeq miRNA WTA (1x96)
Ion Torrent Configurations
916-001-308 HTG EdgeSeq miRNA WTA (2x8)
916-001-108 HTG EdgeSeq miRNA WTA (4x8)
916-001-324 HTG EdgeSeq miRNA WTA (1x24)
916-001-124 HTG EdgeSeq miRNA WTA (4x24)

Product Specifications

miRbase   v20

miRNA Probes




  sRNA (Pol3) RNU47, RNU75, RNY3, SNORA66
  rRNA RPL19, RPS20, RPL27, RSP12
Controls Negative 5 ANT Probes
  Positive 1 IVT Probe

Sample Input

Sample Type Sample Input
FFPE Tissue A single 5 µm FFPE tissue section 
Cells > 3,000 cells
Plasma/Serum > 15 µl
PAXGene 500 µl
Extracted RNA > 25 ng

Learn more about HTG EdgeSeq products and chemistry

HTG EdgeSeq miRNA Expression Profiling
HTG EdgeSeq mRNA Expression Profiling
HTG EdgeSeq Future Applications
HTG EdgeSeq Chemistry


HTG EdgeSeq miRNA Whole Transcriptome Assay sales sheet
HTG EdgeSeq miRNA Whole Transcriptome Assay gene list


Verification of miRNA Expression using Nuclease Protection and Targeted Next-Generation Sequencing (presented at ESHG 2016)
Automated high fidelity miRNA expression profiling using nuclease protection coupled with next generation sequencing

Evaluation of normalization methods for miRNA sequencing data generated with qNPA

HTG's GenomeWeb webinar: New Tools for Biomarker Discovery Promise Personalized Treatment for Rheumatoid Arthritis

​HTG's GenomeWeb webinar: NGS-based miRNA Profiling for Potential Clinical Applications

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For Research Use Only. Not for use in diagnostic procedures.

How to Get It

For further information on the HTG EdgeSeq miRNA Whole Transcriptome Assay, please fill out the below registration form. 

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Last updated: 05/10/2017 - 11:01

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