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
|est. 8-12 x 5 µm tissue sections2
|est. 3-4 x 5 µm tissue sections2
|Cells||> 3,000 cells||10,000 cells||est. 12,500 cells2
|est. 5,000 cells2
|Plasma/Serum||> 15 µl||est. 400 µl4
|est. 500 µl3
|est. 250-500 µl3
|PAXgene||500 µl||est. 100 µl1
|est. 500 µl1
|est. 50 µl1
|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
|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)|
|Common||ACTB, B2M, GAPDH, YWHAZ, PPIA|
|sRNA (Pol3)||RNU47, RNU75, RNY3, SNORA66|
|rRNA||RPL19, RPS20, RPL27, RSP12|
|Controls||Negative||5 ANT Probes|
|Positive||1 IVT Probe|
|Sample Type||Sample Input|
|FFPE Tissue||A single 5 µm FFPE tissue section|
|Cells||> 3,000 cells|
|Plasma/Serum||> 15 µl|
|Extracted RNA||> 25 ng|
Learn more about HTG EdgeSeq products and chemistry
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
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.