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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Electron microscopy for virus identification and virus assemblage characterization Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.eahbab6 | VERVE Net | 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. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_057.pdf | 1 | 2015 | 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 | 2021-04-15 09:15:30 | ||
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Discovering novel genetic polymorphism using VIROME Resource Report Resource Website |
Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack | DOI:10.17504/protocols.io.d6p9dm | VERVE Net, Hurwitz Lab | 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. | , , | http://virome.dbi.udel.edu/ | 1 | 2016 | 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 | 2021-04-15 09:15:31 | ||
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How to use paired-end information for graph decomposition Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | DOI:10.17504/protocols.io.d7p9mm | VERVE Net, Hurwitz Lab | Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab | http://metavelvet.dna.bio.keio.ac.jp/MV.html | 1 | 2016 | 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 | 2021-04-15 09:15:33 | |||
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The abundance and taxonomy of microbes in our meals for three diet types Resource Report Resource Website |
Qianwen Luo | DOI:10.17504/protocols.io.etpbemn | VERVE Net | 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/ | 1 | 2016 | 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 | 2021-04-15 09:15:52 | ||||
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PCR amplification of the SISPA primer denaturing cycles Resource Report Resource Website |
KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN | DOI:10.17504/protocols.io.emfbc3n | VERVE Net | For use in Generating viral metagenomes from the coral holobiont. | , , , | 1 | 2016 | 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 | 2021-04-15 09:15:52 | |||
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A degenerate primer reverse transcriptionpolymerase chain reaction protocol to determine the diversity of picorna-like viruses Resource Report Resource Website |
Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward | DOI:10.17504/protocols.io.dse6bd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | 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. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_193.pdf | 1 | 2015 | 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 | 2021-04-15 09:15:52 | ||
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Phage Buffer Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c5ey3d | VERVE Net, Sullivan Lab | Can be used for diluting or resuspending phage preparations. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2015 | Matthew Sullivan 2015. Phage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5ey3d | 2021-04-15 09:15:37 | |||
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WH7803 PCR Protocol Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.dak2cv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Li Deng 2016. WH7803 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dak2cv | 2021-04-15 09:15:36 | ||||
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Ascorbic-EDTA Buffer Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c8xzxm | VERVE Net, Sullivan Lab | For use in Wet-mount Method for Enumeration of Aquatic Viruses | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | 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 | 2021-04-15 09:15:51 | |||
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Construction of shotgun libraries from RNA virus assemblages Resource Report Resource Website |
Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward | DOI:10.17504/protocols.io.dsi6cd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | 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." | Suttle Lab, Suttle Lab, Suttle Lab | http://www.aslo.org/books/mave/MAVE_193.pdf | 1 | 2015 | 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 | 2021-04-15 09:15:53 | ||
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CviJI Buffer B Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esjbecn | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Buffer B. protocols.io https://dx.doi.org/10.17504/protocols.io.esjbecn | 2021-04-15 09:15:40 | ||||
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Resolving gel buffer (4X) Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.eq3bdyn | VERVE Net | For use in Polyacrylamide Gel System For Electrophoresis Of Proteins. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. Resolving gel buffer (4X). protocols.io https://dx.doi.org/10.17504/protocols.io.eq3bdyn | 2021-04-15 09:15:43 | ||||
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Definitive guide to western blot Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eqwbdxe | VERVE Net | 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. | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Definitive guide to western blot. protocols.io https://dx.doi.org/10.17504/protocols.io.eqwbdxe | 2021-04-15 09:15:43 | |||
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Chlorella Virus Plaque Assay Resource Report Resource Website |
Dr. Steven Wilhelm, Samantha Coy | DOI:10.17504/protocols.io.hgqb3vw | 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 | 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. | , | http://ncv.unl.edu/vanettenlab/Plaque%20assay.pdf | 2 | 2017 | Dr. Steven Wilhelm, Samantha Coy 2017. Chlorella Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.hgqb3vw | 2021-04-15 09:15:41 | ||
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One-step growth curves for Pseudoalteromonas phages Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.den3dd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Natalie Solonenko 2016. One-step growth curves for Pseudoalteromonas phages. protocols.io https://dx.doi.org/10.17504/protocols.io.den3dd | 2021-04-15 09:15:49 | ||||
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DNA Precipitation Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c34yqv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c34yqv | 2021-04-15 09:15:48 | ||||
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Marine Purity Broth Resource Report Resource Website |
Bertillson et al. | DOI:10.17504/protocols.io.dcm2u5 | VERVE Net, Sullivan Lab | Purpose: To test axenic cultures for purity | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bertillson et al. 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.dcm2u5 | 2021-04-15 09:15:45 | |||
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1M Sodium citrate Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c6azad | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 1M Sodium citrate. protocols.io https://dx.doi.org/10.17504/protocols.io.c6azad | 2021-04-15 09:15:45 | ||||
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Plaque assay protocol for Cellulophaga Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddg23v | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Plaque assay protocol for Cellulophaga. protocols.io https://dx.doi.org/10.17504/protocols.io.ddg23v | 2021-04-15 09:15:47 | ||||
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Pellet resuspension Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | DOI:10.17504/protocols.io.dzt76m | VERVE Net | For use in Viral and bacterial isolates, propagation and preparation of stocks. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_019.pdf | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. Pellet resuspension. protocols.io https://dx.doi.org/10.17504/protocols.io.dzt76m | 2021-04-15 09:15:50 |
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