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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...

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Updated: Jun 1, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Using DNA microarrays to assay part function.

Virgil A Rhodius¹, Carol A Gross

¹Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA.

Methods in Enzymology

|May 24, 2011

Summary

This summary is machine-generated.

Synthetic biology enables large genetic circuits, but parts can impact host cells. DNA microarrays systematically assess these impacts, aiding circuit design and optimization.

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Last Updated: Jun 1, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

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Published on: March 15, 2011

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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Area of Science:

Synthetic biology
Molecular biology
Genomics

Background:

Advances in DNA synthesis and assembly accelerate the design of large genetic circuits.
Genetic circuits require diverse components (parts), including regulators and devices, which can affect host cell physiology.
Understanding the host impact of genetic parts is crucial for successful circuit design and fabrication.

Purpose of the Study:

To present a comprehensive methodology for using DNA microarrays to assess the impact of genetic parts on host cells.
To provide readers with the necessary information to catalog genetic part impacts and optimize engineered genetic circuits.
To enable informed design of genetic circuits by considering the potential host effects of individual components.

Main Methods:

Utilizing DNA microarrays for global gene expression monitoring.
Systematic assessment of host cell responses to the expression of genetic circuit parts.
Detailed methodology covering array platform selection, experimental design, sample preparation, and data analysis (preprocessing, normalization, clustering, differential gene expression analysis).
Inclusion of bioinformatic resources and tools for data analysis.

Main Results:

Established a systematic approach to catalog the impact of genetic parts on host cells using DNA microarrays.
Provided a framework for interpreting gene expression data to understand part-host interactions.
Enabled optimization of genetic circuit operation by accounting for part-induced host stresses.

Conclusions:

DNA microarrays are an effective tool for evaluating the host impact of genetic parts in synthetic biology.
Systematic cataloging of part impacts facilitates the design of robust and predictable genetic circuits.
This methodology supports the optimization of engineered genetic circuits for improved performance and host compatibility.