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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: Apr 30, 2026

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR

Published on: July 30, 2011

Absence/presence calling in microarray-based CGH experiments with non-model organisms.

Martijs J Jonker¹, Wim C de Leeuw¹, Marino Marinković²

¹MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS), Faculty of Science (FNWI), University of Amsterdam (UvA), 1098 XH, Amsterdam, the Netherlands Netherlands Bioinformatics Centre (NBIC), 6525 GA, Nijmegen, the Netherlands.

Nucleic Acids Research

|April 29, 2014

Summary

This summary is machine-generated.

This study introduces a new genome analysis method for non-model organisms. It accurately detects copy number variation without needing a reference genome sequence.

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Last Updated: Apr 30, 2026

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In Vivo Modeling of the Morbid Human Genome using Danio rerio

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Published on: August 24, 2013

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Area of Science:

Genomics
Bioinformatics
Comparative Genomics

Background:

Comparative genomic hybridization (CGH) is standard for studying genomic structural variations in model organisms.
Established CGH analysis relies on signal ratios and probe order, limiting its use in non-model organisms with unknown genome structures.

Purpose of the Study:

To develop a novel CGH analysis approach for non-model organisms.
To enable quantification of probe target presence or absence without a reference genome.

Main Methods:

A new analysis method was developed that compares target probe intensities against control probes.
This approach determines the presence or absence of a probe target in an unknown genome.
The method was validated using Staphylococcus aureus MRSA252, achieving high accuracy.

Main Results:

The novel approach demonstrated high success, with receiver operating characteristic area under the curve values exceeding 0.9995.
The method accurately quantifies genome content in unknown samples.
Usability was shown for comparing genome content and validating next-generation sequencing reads in eukaryotic non-model organisms.

Conclusions:

The presented analysis approach is effective for CGH in non-model organisms.
It overcomes limitations of traditional methods by not requiring a reference genome.
This method broadens the application of CGH for genomic studies in diverse organisms.