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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: Jul 14, 2026

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

Expression profiling using affymetrix genechip probe arrays.

Martina Schinke-Braun¹, Jennifer A Couget

¹Novartis Institutes for BioMedical Research, Cambridge, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|June 15, 2007

Summary

This study details Affymetrix GeneChip probe arrays for analyzing gene expression. It covers standard procedures for RNA isolation, target preparation, and quality control for reproducible results.

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Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Microarray expression profiling aids in understanding biological processes, cancer prognosis, and drug target identification.
Affymetrix GeneChip probe arrays offer high-density oligonucleotide analysis for numerous species.
Human and mouse whole-genome arrays can analyze up to 47,000 transcripts and variants.

Purpose of the Study:

To describe standard assay procedures for Affymetrix GeneChip probe arrays.
To detail RNA isolation, target generation, and array processing.
To outline quality control measures for gene expression analysis.

Main Methods:

Utilizing Affymetrix GeneChip probe arrays with perfect match (PM) and mismatch (MM) oligonucleotide pairs.
Standardized protocols for target preparation, hybridization, and processing using the Affymetrix instrument system.
Isolation of total RNA from heart tissue and generation of biotin-labeled targets.

Main Results:

Standardized fabrication and protocols ensure low technical variability and high reproducibility.
The PM/MM design effectively identifies and subtracts nonspecific hybridization and background signals.
Comprehensive quality control measures are essential for reliable expression data.

Conclusions:

Affymetrix GeneChip arrays provide a robust and reproducible platform for large-scale gene expression analysis.
Standardized procedures are critical for accurate and reliable results in expression profiling studies.
This methodology supports advancements in basic biological research and clinical applications like cancer prognosis.