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Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003).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 2015. Electron microscopy for virus identification and virus assemblage characterization. protocols.io https://dx.doi.org/10.17504/protocols.io.eahbab6 Copy   

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Authors: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: This tutorial explains how to use VIROME to discover novel genetic polymorphism from viral metagenome shotgun data. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information.

Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. Discovering novel genetic polymorphism using VIROME. protocols.io https://dx.doi.org/10.17504/protocols.io.d6p9dm Copy   

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Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. How to use paired-end information for graph decomposition. protocols.io https://dx.doi.org/10.17504/protocols.io.d7p9mm Copy   

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Authors: Qianwen Luo
Group: VERVE Net
Summary: This tutorial was based off of the paper The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types. The article provides those interested in bioinformatics, food science, or microbiology information about how to test the abundance and taxonomy of microbes in our daily meals. The step by step procedures covers how the author run this experiment. Source:Lang JM, Eisen JA, Zivkovic AM. (2014) The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ2:e659. https://peerj.com/articles/659/

Proper citation: Qianwen Luo 2016. The abundance and taxonomy of microbes in our meals for three diet types. protocols.io https://dx.doi.org/10.17504/protocols.io.etpbemn 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. PCR amplification of the SISPA primer denaturing cycles. protocols.io https://dx.doi.org/10.17504/protocols.io.emfbc3n Copy   

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Authors: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known about the composition, dynamics, and ecology of the RNA virioplankton. In this protocol, we describe a method to assess RNA virus diversity from seawater.

Proper citation: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward 2015. A degenerate primer reverse transcriptionpolymerase chain reaction protocol to determine the diversity of picorna-like viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dse6bd Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Can be used for diluting or resuspending phage preparations.

Proper citation: Matthew Sullivan 2015. Phage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5ey3d Copy   

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Authors: Li Deng
Group: VERVE Net, Sullivan Lab

Proper citation: Li Deng 2016. WH7803 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dak2cv Copy   

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Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses

Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Ascorbic-EDTA Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c8xzxm Copy   

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Authors: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The following protocol is used to construct shotgun libraries from RNA virus assemblages. This method is designed to detect all RNA viruses, regardless of their genome orientation, and therefore provides a broader assessment of RNA virus diversity compared to the single-gene–based method described in "A degenerate primer reverse transcriptionpolymerase chain reaction–based protocol to determine the diversity of picorna-like viruses."

Proper citation: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward 2015. Construction of shotgun libraries from RNA virus assemblages. protocols.io https://dx.doi.org/10.17504/protocols.io.dsi6cd Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Buffer B. protocols.io https://dx.doi.org/10.17504/protocols.io.esjbecn Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. Resolving gel buffer (4X). protocols.io https://dx.doi.org/10.17504/protocols.io.eq3bdyn Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Summary: Western blotting uses specific antibodies to identify proteins that have been separated based on size by gel electrophoresis. The immunoassay uses a membrane made of nitrocellulose or PVDF (polyvinylidene fluoride). The gel is placed next to the membrane and application of an electrical current induces the proteins to migrate from the gel to the membrane. The membrane can then be further processed with antibodies specific for the target of interest, and visualized using secondary antibodies and detection reagents.

Proper citation: David Dunigan and Irina Agarkova 2016. Definitive guide to western blot. protocols.io https://dx.doi.org/10.17504/protocols.io.eqwbdxe Copy   

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Authors: Dr. Steven Wilhelm, Samantha Coy
Group: VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/ Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Chlorella Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.hgqb3vw Copy   

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Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab

Proper citation: Natalie Solonenko 2016. One-step growth curves for Pseudoalteromonas phages. protocols.io https://dx.doi.org/10.17504/protocols.io.den3dd Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c34yqv Copy   

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Authors: Bertillson et al.
Group: VERVE Net, Sullivan Lab
Summary: Purpose: To test axenic cultures for purity

Proper citation: Bertillson et al. 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.dcm2u5 Copy   

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

Proper citation: Matthew Sullivan Lab 2015. 1M Sodium citrate. protocols.io https://dx.doi.org/10.17504/protocols.io.c6azad Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Plaque assay protocol for Cellulophaga. protocols.io https://dx.doi.org/10.17504/protocols.io.ddg23v Copy   

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Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net
Summary: For use in Viral and bacterial isolates, propagation and preparation of stocks.

Proper citation: André M. Comeau and Rachel T. Noble 2016. Pellet resuspension. protocols.io https://dx.doi.org/10.17504/protocols.io.dzt76m Copy   

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