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High reproducibility using sodium hydroxide-stripped long oligonucleotide DNA microarrays
Zhiyuan Hu1, Melissa Troester, Charles M Perou
1University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA.
Biotechniques
|February 1, 2005
Summary
Researchers developed a method to strip and reuse long oligonucleotide microarrays, reducing costs. Replicate experiments showed high reproducibility after one reuse, making these arrays reliable for a second hybridization.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Long oligonucleotide (60- to 70-mer) microarrays are increasingly used for two-color experiments.
- RNA amplification is employed when limited mRNA is available for microarray hybridization.
Purpose of the Study:
- To develop a method for stripping and reusing glass-based oligonucleotide microarrays.
- To assess the reproducibility and reliability of stripped microarrays for subsequent experiments.
Main Methods:
- Utilized selective RNA degradation under alkaline conditions to strip fluorescent RNA from DNA oligonucleotide probes.
- Performed replicate microarray experiments on virgin and stripped arrays using the same samples.
Main Results:
- Developed a reliable method to strip and reuse oligonucleotide microarrays once without compromising data quality.
- Intraclass correlation (ICC) between virgin and stripped arrays ranged from 0.90-0.98, comparable to replicate virgin arrays.
- Stripped arrays demonstrated high reproducibility for a second hybridization experiment.
Conclusions:
- Once-stripped oligonucleotide microarrays are usable and reliable, enabling a second hybridization.
- This stripping method offers a cost-effective solution for microarray experiments.
- The technique supports the sustainable use of valuable microarray resources.
