Hybridization buffer systems impact the quality of filter array data

Journal of Pharmacological and Toxicological Methods
Jie LiuMichael P Waalkes

Abstract

cDNA microarray technology has greatly facilitated mechanistic studies in pharmacology and toxicology. A clean hybridization with minimal background is critical for successful microarray analysis and is highly desired. However, clean hybridization alone is not enough; verification is needed. Total RNA was isolated from the livers of acetaminophen-intoxicated mice and was subjected to cDNA microarray analyses using ExpressHyb, ULTRArrayHyb or MicroHyb on nylon membranes. Real-time RT-PCR analyses were performed for verification. We have demonstrated in this paper that hybridization systems can significantly impact the quality of array data. MicroHyb produced very clean hybridizations, but some results could not be confirmed by real-time RT-PCR and in accord with biological responses. The hybridization images from ExpressHyb were not always clean, but were reliable. The sensitivity of ULTRArrayHyb was moderate. This study has indicated the importance of selecting hybridization buffers in membrane arrays and recommended real-time RT-PCR for follow-up analysis. Gene expression changes should also be correlated with biological significance.

References

Jun 26, 2001·Journal of Biochemical and Molecular Toxicology·N J Walker
Apr 20, 2002·Science·Nigel J Walker
Jan 24, 2003·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jie LiuLarry K Keefer
Dec 24, 2003·Toxicological Sciences : an Official Journal of the Society of Toxicology·Jie LiuMichael P Waalkes

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Citations

Aug 30, 2005·BMC Bioinformatics·Stanislav O ZakharkinGrier P Page
Aug 15, 2006·Biomolecular Engineering·Catherine SitumaSteven A Soper
Dec 4, 2008·Critical Reviews in Biotechnology·Jai Prakash MuyalHeinz Fehrenbach

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