Laboratory procedures to generate viral metagenomes

This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several con...

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Vydané v:	Nature protocols Ročník 4; číslo 4; s. 470 - 483
Hlavní autori:	Thurber, Rebecca V, Haynes, Matthew, Breitbart, Mya, Wegley, Linda, Rohwer, Forest
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London Nature Publishing Group UK 01.04.2009 Nature Publishing Group
Predmet:	Acids Analytical Chemistry Biological Techniques Biomedical and Life Sciences Computational Biology/Bioinformatics Consortia DNA Viruses - genetics DNA Viruses - isolation & purification Genetic aspects Genome, Viral Genomic Library Genomics - methods Life Sciences Methods Microarrays Nucleic Acid Amplification Techniques Nucleic acids Nucleotide sequence Organic Chemistry Polyethylene glycol Protocol Separation Ultracentrifugation Virion - genetics Virion - isolation & purification Virus Cultivation Viruses United States Florida United States > US
ISSN:	1754-2189, 1750-2799, 1750-2799
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Popis
Shrnutí:	This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several concentration, purification, extraction, sequencing and heuristic bioinformatic methods. No single technique can provide an all-inclusive approach, and therefore the protocols presented here will be discussed in terms of hypothetical projects. However, care must be taken to individualize each step depending on the source and type of viral-particles. This protocol is a description of the processes we have successfully used to: (i) concentrate viral particles from various types of samples, (ii) eliminate contaminating cells and free nucleic acids and (iii) extract, amplify and purify viral nucleic acids. Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in ∼1 week.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1754-2189 1750-2799 1750-2799
DOI:	10.1038/nprot.2009.10