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DNA Microarrays

DNA Microarrays

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: Dec 21, 2025

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

Published on: August 3, 2011

Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays.

Maxwell B Nagarajan¹, Augusto M Tentori¹, Wen Cai Zhang²

¹1Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.

Microsystems & Nanoengineering

|May 19, 2020

Summary

We developed a new method for spatially resolved microRNA (miRNA) measurements in FFPE tissues. This technique can quantify tissue heterogeneities and aid in biomarker-based diagnostics for diseases like lung cancer.

Keywords:

Chemistry Engineering

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Last Updated: Dec 21, 2025

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

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Published on: August 3, 2011

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Published on: April 14, 2015

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as A Novel Detection and Quantification Method

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as A Novel Detection and Quantification Method

Published on: October 7, 2025

Area of Science:

Biomedical Engineering
Molecular Biology
Cancer Research

Background:

Spatially resolved gene expression is crucial for medical studies and companion diagnostics.
Current technologies for quantifying and multiplexing gene expression in tissues are limited.
MicroRNA (miRNA) analysis in formalin-fixed, paraffin-embedded (FFPE) tissues presents unique challenges.

Purpose of the Study:

To present a novel method for spatially resolved and multiplexed miRNA measurements.
To enable quantification of miRNA expression directly from FFPE tissue sections.
To demonstrate the application of this technology in a relevant cancer model.

Main Methods:

Utilized nanoliter well arrays to pixelate FFPE tissue sections.
Employed photopatterned hydrogels for quantitative miRNA detection.
Applied the method to a genetically engineered mouse model for non-small cell lung cancer (K-ras^LSL-G12D/+; p53^fl/fl).

Main Results:

Successfully performed spatially resolved and multiplexed miRNA measurements from FFPE tissue.
Identified differentially expressed miRNAs within tumors of the mouse model.
Demonstrated the ability to quantify miRNA heterogeneities within the tissue sample.

Conclusions:

The developed technology allows for precise, spatially resolved miRNA quantification in FFPE tissues.
This method can reveal tissue heterogeneities important for understanding disease.
The technology holds potential for developing informed, biomarker-based diagnostics.