title: Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.
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 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.
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Joy D
authors.initials: JD
authors.lastname: Van Nostrand
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Huaqin
authors.initials: H
authors.lastname: Yin
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Tong
authors.initials: T
authors.lastname: Yuan
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA. jzhou@ou.edu.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D001419:Bacteria / Q000235:genetics; D004352:Drug Resistance, Microbial / Q000235:genetics; D005658:Fungi / Q000145:classification / Q000235:genetics; D014644:Genetic Variation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012988:Soil Microbiology; D014780:Viruses / Q000145:classification / Q000235:genetics
keywords: Fluorescent labeling; Functional gene array; GeoChip; Hybridization; Microbial communities; Microbial ecology; Whole community genome amplification