Genomic Analysis
SmartRNAplex™ microRNA Profiling Assays

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The latest application note describes how the SmartRNAplex™ Assay is used for multiplexed quantitation of miRNA expression in HER-2-positive tumor breast tissues and adjacent normal (HER-2-negative) breast tissue samples derived from the same patient.

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SmartRNAplex miRNA Assays are your benchtop solution for miRNA profiling
Particle anatomy in the SmartRNAplex™ Assay

Find the miRNAs that Matter.

Have you ever wondered if microRNAs are key control molecules in YOUR system? If so, which miRNAs really matter?

SmartRNAplex miRNA Assays are your benchtop solution for miRNA profiling, using a familiar protocol, and simple acquisition software, you can:
  • Configure nearly ANY number of miRNA targets (between 10 and 68)
  • Start with ANY sample type – blood, plasma, cell lysates, or FFPE tissue
  • Process ANY number of samples from 1-96
  • Use ANY flow cytometer (optimized for the guava easyCyte™ Flow Cytometer (96 samples) and the Muse® Cell Analyzer)
Get more plex than qPCR, and run more samples than microarrays.

What's Smart?

SmartRNAplex microRNA Assays use proprietary Firefly™ technology, which exploits uniquely encoded hydrogel particles developed by innovators at Firefly BioWorks.” The Firefly™ hydrogel particles are hydrophilic, bio-inert, flexible and porous, allowing target molecules to diffuse and bind in a unique nanoscale three-dimensional scaffold. As a result, more target miRNAs bind per particle, giving you:

  • Maximum signal
  • Larger dynamic range
  • Decreased background
After mixing the samples, “hybridization” of miRNA targets confirms target recognition. Subsequently, each successful hybridized particle will then bind a fluorescent label, resulting in fluorescence as detected by a flow cytometer.
Molecular mechanism of SmartRNAplex assay. Uniquely encoded hydrogel particles (containing specific miRNA sequences and barcodes for identification) are mixed with testing samples in a 96-well filtration plate. After mixing the samples, “hybridization” of miRNA targets confirms target recognition. Subsequently, each successful hybridized particle will then bind a fluorescent label, resulting in fluorescence as detected by a flow cytometer. Non-complementary strands or inadequate hybridization will not allow binding of a fluorescent label, resulting in no fluorescence. This confirms target specificity within the assay, as well as the level of miRNA expression for each testing sample.
About Firefly™ BioWorks
Firefly™ BioWorks develops integrated solutions for accelerating scientific discovery. The Firefly™ technology allows industrial, academic and clinical scientists to access powerful custom, multiplex assays on any standard laboratory instrumentation.

Firefly BioWorks
Read references for Firefly™ technology:
  • Chapin, S.C., Pregibon, D.C. and Doyle, P.S. Rapid microRNA Profiling on Encoded Gel Microparticles.
    Angew. Chem. Int. Ed. 50 2289 (2011) (PDF)

  • Chapin, S.C. and Doyle, P.S. Ultrasensitive Multiplexed MicroRNA Quantification on Encoded Gel Microparticles Using Rolling Circle Amplification.
    Analytical Chemistry 83, 7179 (2011) (PDF)

  • Appleyard, D., Chapin, S.C., Srinivas, R. and Doyle, P.S. Barcoded Hydrogel Microparticles for Protein Detection: Synthesis, Assay, and Scanning.
    Nature Protocols 6, 1761 (2011) (PDF)

  • Pregibon, D.C. and Doyle, P.S. Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification.
    Analytical Chemistry 81, 4873 (2009) (PDF)

  • Pregibon, D.C., Toner, M. and Doyle, P.S. Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis.
    Science 315, 1393 (2007) (PDF)