Hybridization buffer systems impact the quality of filter array data.

Jie Liu; Nigel Walker; Michael P Waalkes

doi:10.1016/j.vascn.2004.02.001

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Hybridization buffer systems impact the quality of filter array data.

Jie Liu·Nigel Walker·Michael P Waalkes

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Abstract

INTRODUCTION: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.

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Acetaminophen Analgesics, Non-Narcotic Animals Buffers DNA Primers Liver Male Mice Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis RNA, Messenger Reverse Transcriptase Polymerase Chain Reaction Comparative Study Journal Article

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Jie Liu, Nigel Walker, Michael P Waalkes. Hybridization buffer systems impact the quality of filter array data.. https://doi.org/10.1016/j.vascn.2004.02.001

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