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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Related Experiment Video

Updated: Feb 26, 2026

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
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Determination of absolute expression profiles using multiplexed miRNA analysis.

Yunke Song1, Duncan Kilburn2, Jee Hoon Song3

  • 1Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America.

Plos One
|July 14, 2017
PubMed
Summary
This summary is machine-generated.

Ligo-miR offers precise microRNA (miRNA) quantification, reducing reliance on biological controls for accurate gene expression analysis and disease biomarker discovery. This multiplex assay enables sensitive, reliable measurement of miRNA copy numbers and differential expression changes.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Accurate microRNA (miRNA) expression measurement is essential for understanding gene regulation and identifying disease biomarkers.
  • Reliable normalization is crucial to account for biological and technical variability in miRNA expression studies.
  • Existing methods often depend on biological controls, introducing potential variance.

Purpose of the Study:

  • To introduce Ligo-miR, a novel multiplex assay for rapid, absolute quantification of miRNA copy numbers.
  • To reduce dependence on biological controls in miRNA expression analysis.
  • To demonstrate the utility of Ligo-miR for sensitive and accurate miRNA profiling.

Main Methods:

  • Ligo-miR utilizes a 2-step ligation process to generate length-coded DNA products.
  • Quantification is achieved through various DNA sizing methods.
  • The assay was validated through sensitivity, specificity, and differential expression measurements.

Main Results:

  • Ligo-miR achieves a sensitivity of 20 copies per cell.
  • The assay accurately distinguishes between closely related miRNAs and detects fold-changes as low as 1.2.
  • Benchmarking showed high correlation with microarray and TaqMan qRT-PCR.

Conclusions:

  • Ligo-miR provides a robust method for absolute miRNA copy number quantification.
  • The assay offers high sensitivity and accuracy for detecting differential miRNA expression.
  • Ligo-miR facilitates layered insights into expression profiles using copy number analysis in various cell lines.