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Authors: Qiagen
Group: VERVE Net, Sullivan Lab
Summary: This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A

Proper citation: Qiagen 2015. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.c49yz5 Copy   

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Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation

Proper citation: Nick Tang 2016. VBRC Base By Base: Import genome sequences from Virology.ca viral databases. protocols.io https://dx.doi.org/10.17504/protocols.io.ecjbaun Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stocks (liquid assay)"

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Lysate titer. protocols.io https://dx.doi.org/10.17504/protocols.io.dqn5vd Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. g23 T4-type (myovirus) PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfq3mv Copy   

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Authors: Rex Malmstrom
Group: VERVE Net, Sullivan Lab
Summary: This is a storage solution that stabilizes and protectsRNA while inactivating RNase

Proper citation: Rex Malmstrom 2015. RNAlater Recipe. protocols.io https://dx.doi.org/10.17504/protocols.io.c56y9d Copy   

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Authors: Benjamin Bolduc
Group: VERVE Net, Sullivan Lab, iVirus
Summary: Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter.

Proper citation: Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gv2bw8e Copy   

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Authors: Janice E. Lawrence and Grieg F. Steward
Group: VERVE Net
Summary: Ultracentrifugation provides a means to concentrate, analyze, and purify viruses in solution, and therefore represents an invaluable tool for aquatic virologists. This protocol provides a method for purification of viruses from culture lysates from natural water samples.

Proper citation: Janice E. Lawrence and Grieg F. Steward 2015. Purification of viruses from culture lysates. protocols.io https://dx.doi.org/10.17504/protocols.io.d2t8em Copy   

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Authors: Carolina Cadena
Group: VERVE Net
Summary: This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format.  Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72

Proper citation: Carolina Cadena 2016. Detecting Fungal Infections in Almonds. protocols.io https://dx.doi.org/10.17504/protocols.io.etnbeme Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Dot Blot Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.etibeke Copy   

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Authors: KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN
Group: VERVE Net
Summary: For use in Generating viral metagenomes from the coral holobiont.

Proper citation: KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN 2016. MECH step CsCl density gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.ek5bcy6 Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Supplement to seawater for growth of cyanobacteria.

Proper citation: Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io https://dx.doi.org/10.17504/protocols.io.c77zrm Copy   

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Authors: Grieg F. Steward and Alexander I. Culley
Group: VERVE Net
Summary: The traditional phenol extraction procedure, based on early work by Kirby (1957) and elaborated in most modern protocol compendia, yields very clean nucleic acids suitable for a variety of downstream applications. This extraction method is coupled with a routine alcohol precipitation step to allow buffer exchange, removal of trace amounts of chloroform, and concentration of nucleic acids (Sambrook and Russell 2001).This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information.

Proper citation: Grieg F. Steward and Alexander I. Culley 2015. Phenol-chloroform extraction with ethanol precipitation. protocols.io https://dx.doi.org/10.17504/protocols.io.dsb6am Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: Multiwell plates are convenient for isolating cyanophages from environmental samples using the liquid bioassay approach (Table 1). This protocol describes a typical procedure (96-well assay) used to detect and isolate cyanophages from marine samples that lyses Synechococcus sp. strain DC2 (also known as CCMP1334 or WH7803). Using this method, greater than 105 lytic phages per milliliter of seawater have been detected in the Gulf of Mexico (Suttle and Chan 1994) that lyses this permissive target host.

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Isolation of cyanophages by liquid bioassays. protocols.io https://dx.doi.org/10.17504/protocols.io.dp25qd Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Summary: PBCV-1 is a large plaque virus (approximately 2-3 mm in diameter).  The plaque size of the viruses reflects the length of the virus replication cycle.  PBCV-1 has a life cycle of about 6-8 hours.  When titering you should use plates that were poured no more than 1 day before the time of use.  Variable plaque formation will result if fresh plates are not used.  (This is similar to a phage phenomenon.)  Pyrex petri dishes do give more uniform plaque formation versus the plastic, however this is not so critical as with slower growing NC64A viruses.

Proper citation: David Dunigan and Irina Agarkova 2016. PBCV-1 Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.estbeen Copy   

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Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation

Proper citation: Nick Tang 2016. VBRC Base By Base: Switching between Mouse Modes. protocols.io https://dx.doi.org/10.17504/protocols.io.ecpbavn Copy   

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Authors: Rohan Sachdeva,  Cheryl Chow 
Group: VERVE Net, Fuhrman Lab
Summary: Reference: Fuhrman et al, 1988. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies. AEM 54(6), 1426‐1429

Proper citation: Rohan Sachdeva,  Cheryl Chow  2015. SPOT DNA Extraction from 142mm Durapore 0.22µm Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.dmi44d Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Formulation of FES Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.eucbesw Copy   

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Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information.

Proper citation: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Electron Microscopy of Haloviruses. protocols.io https://dx.doi.org/10.17504/protocols.io.ebbbain Copy   

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Authors: Matt Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matt Sullivan Lab 2016. Preparation of Tara Sample DNA From Iron-Chloride Precipitates. protocols.io https://dx.doi.org/10.17504/protocols.io.c24ygv Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for detecting Human Polyomaviruses (HPyVs) in our virome and whole metagenome datasets. For genome reference, download the HPyV genomes (in fasta format) from NCBI (nucleotide) using the search terms "Human Polyomavirus" AND "Complete Genome". This is used in the rest of the analyses. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script P6: HPyV Detection. protocols.io https://dx.doi.org/10.17504/protocols.io.efxbbpn Copy   

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