Tips on hybridizing, washing, and scanning affymetrix microarrays

Area of Science:

• Biotechnology
• Molecular Biology
• Genomics

Background:

• Affymetrix, Inc. developed a commercial system for microarray analysis in the late 1990s.
• The system emphasized ease of operation and reproducibility through automation and standardization.
• Key components included specialized cassettes, fluidics stations, hybridization ovens, and scanners.

Purpose of the Study:

• To provide a skeleton protocol for the Affymetrix microarray system.
• To identify and address potential pitfalls in the protocol.
• To augment existing protocols provided by Affymetrix for enhanced user guidance.

Main Methods:

• Utilizing the Affymetrix commercial system for microarray hybridization, washing, and scanning.
• Employing automated fluidics stations for fluid handling within array cassettes.
• Implementing a specialized rotating hybridization oven and scanner.

Main Results:

• The Affymetrix system's popularity is attributed to its automation and standardization.
• A protocol framework is presented, outlining key steps and considerations.
• Potential challenges and their mitigation strategies are identified.

Conclusions:

• The Affymetrix system remains a popular choice for microarray analysis due to its robust design.
• This protocol serves as a valuable supplement for researchers using the Affymetrix platform.
• Understanding potential pitfalls can lead to more successful and reproducible microarray experiments.