Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.
Microbial Environmental Genomics (MEG)
Methods in molecular biology, January 2016
Van Nostrand, Joy D, Yin, Huaqin, Wu, Liyou, Yuan, Tong, Zhou, Jizhong, Joy D. Van Nostrand, Huaqin Yin, Liyou Wu, Tong Yuan, Jizhong Zhou
Francis Martin, Stephane Uroz
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 specific for fungi, protists, and viruses. Here, we briefly 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 amplification, labeling, and hybridization of samples to the GeoChip.
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