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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: Jun 3, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

DNA microarrays: sample quality control, array hybridization and scanning.

Elva Diaz¹, Gustavo A Barisone

¹Department of Pharmacology, University of California, Davis, USA.

Journal of Visualized Experiments : Jove

|March 30, 2011

Summary

This study details reproducible microarray protocols for brain tumor tissue, ensuring high-quality RNA for accurate gene expression profiling. These methods enable precise identification of differentially expressed genes in various conditions.

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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

High-Density DNA and RNA microarrays - Photolithographic Synthesis, Hybridization and Preparation of Large Nucleic Acid Libraries

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Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Published on: August 10, 2009

Area of Science:

Neuroscience
Molecular Biology
Genomics

Background:

Microarray expression profiling is crucial for understanding gene activity in neural tissues across development and disease states.
High-quality RNA isolation and amplification are essential prerequisites for successful gene expression analysis.
Reproducible protocols are needed for reliable microarray experiments, particularly with challenging samples like brain tumors.

Purpose of the Study:

To describe detailed protocols for reproducible microarray experiments using brain tumor tissue.
To establish quality control measures for RNA samples using Agilent's 2100 Bioanalyzer.
To enable accurate identification of differentially expressed genes in experimental conditions.

Main Methods:

Quality control of isolated RNA using Agilent's 2100 Bioanalyzer.
RNA amplification and dual-color labeling (Cy3 for experimental, Cy5 for reference) via reverse transcription and in vitro transcription.
Hybridization of labeled complementary RNA (cRNA) to Agilent's 4x44 K arrays for competitive analysis.

Main Results:

The described protocols ensure reproducible microarray data from brain tumor tissue.
Agilent's 2100 Bioanalyzer provides quantitative RNA quality assessment.
Dual-color competitive hybridization allows accurate measurement of relative mRNA abundance and identification of differential gene expression.

Conclusions:

The presented protocols facilitate reproducible gene expression profiling in brain tumor research.
Accurate RNA quality control is paramount for reliable microarray results.
Dual-color microarray hybridization enhances the precision of detecting subtle changes in gene expression patterns.