Hybridization of environmental microbial community nucleic acids by geochip

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Abstract

Functional gene arrays, like the GeoChip, allow for the study of tens of thousands of genes in a single assay. The GeoChip array (5.0) contains probes for genes involved in geochemical cycling (N, C, S, and P), metal homeostasis, stress response, organic contaminant degradation, antibiotic resistance, secondary metabolism, and virulence factors as well as genes specifi c for fungi, protists, and viruses. Here, we briefl y describe GeoChip design strategies (gene selection and probe design) and discuss minimum quantity and quality requirements for nucleic acids. We then provide detailed protocols for amplifi cation, labeling, and hybridization of samples to the GeoChip.

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Van Nostrand, J. D., Yin, H., Wu, L., Yuan, T., & Zhou, J. (2016). Hybridization of environmental microbial community nucleic acids by geochip. In Methods in Molecular Biology (Vol. 1399, pp. 183–196). Humana Press Inc. https://doi.org/10.1007/978-1-4939-3369-3_11

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