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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Viruses Purification of Perkinsus spp. Resource Report Resource Website |
Mathieu LAZARE | DOI:10.17504/protocols.io.er9bd96 | VERVE Net, Martínez Martinez Lab | The purpose of this protocol is to isolate and characterize viruses that infect P.olseni, P.marinus. | 3 | 2016 | Mathieu LAZARE 2016. Viruses Purification of Perkinsus spp.. protocols.io https://dx.doi.org/10.17504/protocols.io.er9bd96 | 2021-04-15 09:16:22 | ||||
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Isolation of Haloviruses from Natural Waters Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.ebcbaiw | VERVE Net | 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 | 2016 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Isolation of Haloviruses from Natural Waters. protocols.io https://dx.doi.org/10.17504/protocols.io.ebcbaiw | 2021-04-15 09:16:23 | ||
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Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dem3c5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io https://dx.doi.org/10.17504/protocols.io.dem3c5 | 2021-04-15 09:16:47 | ||||
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Cellulophaga 38:1 Lytic Gene PCR Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfz3p5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga 38:1 Lytic Gene PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dfz3p5 | 2021-04-15 09:16:47 | ||||
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DTT solution Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.erabd2e | VERVE Net | University of Nebraska | 1 | 2016 | David Dunigan and Irina Agarkova 2016. DTT solution. protocols.io https://dx.doi.org/10.17504/protocols.io.erabd2e | 2021-04-15 09:16:44 | ||||
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SYBR Green Assay Resource Report Resource Website |
Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman | DOI:10.17504/protocols.io.djg4jv | VERVE Net, Fuhrman Lab | The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from:Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc. 2007;2(2):269-76.Please see the full manuscript for more details. | Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab | http://www.nature.com/nprot/journal/v2/n2/full/nprot.2007.6.html | 1 | 2015 | Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman 2015. SYBR Green Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.djg4jv | 2021-04-15 09:16:46 | ||
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0.1M EDTA-0.2M MgCl2-0.2M Ascorbate Buffer Resource Report Resource Website |
Seth John, Bonnie Poulos, Christine Schirmer | DOI:10.17504/protocols.io.c2yyfv | VERVE Net, Sullivan Lab | Preparation of iron chloride resuspension buffer using disodium EDTA dihydrate and magnesium chloride in Tris buffer. | 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 | 2015 | Seth John, Bonnie Poulos, Christine Schirmer 2015. 0.1M EDTA-0.2M MgCl2-0.2M Ascorbate Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c2yyfv | 2021-04-15 09:16:24 | |||
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NaCl Sodium Chloride Buffer Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c64zgv | VERVE Net, Sullivan Lab | . | 1 | 2016 | Matthew Sullivan 2016. NaCl Sodium Chloride Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c64zgv | 2021-04-15 09:16:45 | ||||
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Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek4bcyw | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ek4bcyw | 2021-04-15 09:16:49 | ||||
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Script R3: Quality Control Statistics Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.eh9bb96 | VERVE Net, Club Grice | This protocol outlines the quality control analysis measuring the percent relative abundance of 16S rRNA levels in the virome and whole metagenome, as well as the number of virome sequences mapping to the whole metagenome, and vice versa. These measures are used to validate the quality of the sequence datasets. 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. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R3: Quality Control Statistics. protocols.io https://dx.doi.org/10.17504/protocols.io.eh9bb96 | 2021-04-15 09:16:28 | |
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Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy Resource Report Resource Website |
Curtis A. Suttle and Jed A. Fuhrman | DOI:10.17504/protocols.io.dpy5pv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | This is a protocol from: Suttle, C. A. and J. A. Fuhrman. 2010. Chapter 15: Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy. 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 | http://www.aslo.org/books/mave/MAVE_145.pdf | 1 | 2015 | Curtis A. Suttle and Jed A. Fuhrman 2015. Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.dpy5pv | 2021-04-15 09:16:28 | ||
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0.025M NaH2PO4·H2O Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c8czsv | VERVE Net, Sullivan Lab | Supplement to seawater for growth of cyanobacteria. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.025M NaH2PO4·H2O. protocols.io https://dx.doi.org/10.17504/protocols.io.c8czsv | 2021-04-15 09:16:26 | |||
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SOB medium Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eq8bdzw | VERVE Net | University of Nebraska | 1 | 2016 | David Dunigan and Irina Agarkova 2016. SOB medium. protocols.io https://dx.doi.org/10.17504/protocols.io.eq8bdzw | 2021-04-15 09:16:55 | ||||
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CviJI Buffer A Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.esibece | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | David Dunigan and Irina Agarkova 2016. CviJI Buffer A. protocols.io https://dx.doi.org/10.17504/protocols.io.esibece | 2021-04-15 09:16:55 | ||||
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Titration of AmPure XP Beads for Removal of Fragments Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c52y8d | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Titration of AmPure XP Beads for Removal of Fragments . protocols.io https://dx.doi.org/10.17504/protocols.io.c52y8d | 2021-04-15 09:16:54 | ||||
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Cellulophaga growth reading Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dpa5id | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io https://dx.doi.org/10.17504/protocols.io.dpa5id | 2021-04-15 09:16:31 | |||
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VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search) Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.eczbax6 | VERVE Net, Upton-Lab | 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 | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search). protocols.io https://dx.doi.org/10.17504/protocols.io.eczbax6 | 2021-04-15 09:16:54 | ||
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Top agarose Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqh5t5 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | For use in "Isolation of cyanophages by plaque assyays" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Top agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.dqh5t5 | 2021-04-15 09:16:54 | |||
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SYBR Gold Working Stock Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c82zyd | 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. SYBR Gold Working Stock. protocols.io https://dx.doi.org/10.17504/protocols.io.c82zyd | 2021-04-15 09:16:36 | |||
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Enumerating algal viruses by flow cytometry Resource Report Resource Website |
Amy Zimmerman | DOI:10.17504/protocols.io.fccbisw | VERVE Net, Worden Lab | Purpose: To quantify virus-like particles in culture or environmental samples.Host cells and virus-like particles are enumerated from the same glutaraldehyde-fixed sample. For virus counts, an aliquot is diluted in 0.02-µm-filtered TE buffer prior to staining with SYBR Green I nucleic acid dye to improve staining efficiency and ensure an appropriately low event rate in the instrument. An unstained aliquot of sample is run for host cell counts. | Monterey Bay Aquarium Research Institute | 1 | 2016 | Amy Zimmerman 2016. Enumerating algal viruses by flow cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.fccbisw | 2021-04-15 09:16:39 |
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