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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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Updated: Mar 19, 2026

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Published on: March 1, 2017

Thermodynamically optimal whole-genome tiling microarray design and validation.

Hyejin Cho¹, Hui-Hsien Chou^2,3

¹Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.

BMC Research Notes

|June 15, 2016

Summary

This summary is machine-generated.

A new whole-genome tiling microarray design method optimizes probe selection for maximum coverage and specificity. This approach, using thermodynamic analysis, enables the detection of novel RNA transcripts in annotated and unannotated species.

Keywords:

Hybridization Microarray validation PICKY software Prokaryote transcriptome Thermodynamics Tiling microarray design

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Last Updated: Mar 19, 2026

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Microarrays interrogate whole transcriptomes but standard designs require gene annotations, limiting their use for novel transcripts or unannotated species.
Whole-genome tiling microarrays, designed from genomic sequences alone, can detect known and novel RNA transcripts.
Current tiling microarray design faces challenges in balancing probe specificity and genome coverage due to limitations in thermodynamic analysis.

Purpose of the Study:

To develop a novel whole-genome tiling microarray design method.
To optimize probe selection for maximum genome coverage while maintaining specificity.
To enable the detection of novel RNA transcripts in various species.

Main Methods:

Utilized whole-genome thermodynamic analysis software (PICKY) for tiling microarray design.
Focused on achieving maximum genome coverage within thermodynamic constraints.
Ensured selected probes had optimal melting temperature separation between targets and non-targets.

Main Results:

Achieved thermodynamically optimal tiling microarrays with maximum whole-genome coverage.
Designed microarrays where all probes shared a consistent melting temperature separation range.
Demonstrated that no additional probes could be added without compromising microarray specificity.

Conclusions:

A new whole-genome tiling microarray design method was successfully developed and validated.
The method allows for the creation of thermodynamically optimal microarrays.
The design approach was experimentally confirmed using microarrays for Escherichia coli and Agrobacterium tumefaciens.