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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Vydáno v:Nature protocols Ročník 4; číslo 4; s. 470 - 483
Hlavní autoři: Thurber, Rebecca V, Haynes, Matthew, Breitbart, Mya, Wegley, Linda, Rohwer, Forest
Médium: Journal Article
Jazyk:angličtina
Vydáno: London Nature Publishing Group UK 01.04.2009
Nature Publishing Group
Témata:
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.
Bibliografie:ObjectType-Article-1
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ISSN:1754-2189
1750-2799
1750-2799
DOI:10.1038/nprot.2009.10