GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

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A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. ... continued below

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He, Z.; Deng, Y.; Van Nostrand, J.D.; Tu, Q.; Xu, M.; Hemme, C.L. et al. April 1, 2010.

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A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

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  • Journal Name: The ISME Journal; Journal Issue: published online, doi:10.1038/ismej.2010.46; Related Information: Journal Publication Date: 2010

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  • Report No.: LBNL-3402E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 983269
  • Archival Resource Key: ark:/67531/metadc1014898

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Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • April 1, 2010

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  • Oct. 14, 2017, 8:36 a.m.

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  • Oct. 17, 2017, 6:13 p.m.

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He, Z.; Deng, Y.; Van Nostrand, J.D.; Tu, Q.; Xu, M.; Hemme, C.L. et al. GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity, article, April 1, 2010; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc1014898/: accessed January 18, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.