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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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SYBR Staining - Jenn's Method Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.c63zgm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. SYBR Staining - Jenn's Method. protocols.io https://dx.doi.org/10.17504/protocols.io.c63zgm | 2021-04-15 09:16:28 | ||||
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Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dep3dm | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.dep3dm | 2021-04-15 09:16:55 | |||
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Urea/SDS Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.deh3b5 | VERVE Net, Sullivan Lab | For use in "FASP Kit Protocol-OrNL Developed for Bacteriophage" | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Kristin Corrier/Nathan VerBerkmoes 2016. Urea/SDS Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.deh3b5 | 2021-04-15 09:16:55 | |||
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96-well DNA Extraction Protocol from 25mm 0.2µm filters Resource Report Resource Website |
Virginia Rich, DeLong Lab | DOI:10.17504/protocols.io.c4hyt5 | VERVE Net, Sullivan Lab | As used in Rich, Konstantinidis, and DeLong. 2008. Rich VI., Konstantinidis K., DeLong EF. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. http://www.ncbi.nlm.nih.gov/pubmed/18028413. Environ. Microbiol., 2008 Feb;10(2):506-21. Epub 2007 Nov 19. | Matthew Sullivan Lab, University of Arizona, Ohio State University, Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Virginia Rich, DeLong Lab 2016. 96-well DNA Extraction Protocol from 25mm 0.2µm filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c4hyt5 | 2021-04-15 09:16:30 | |||
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Time 0 growth reading using a plate reader Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dw47gv | VERVE Net, Sullivan Lab | For use in "One-step growth curve for Cyanophage" | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Time 0 growth reading using a plate reader. protocols.io https://dx.doi.org/10.17504/protocols.io.dw47gv | 2021-04-15 09:16:31 | |||
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Preparation of Denaturing Agarose Gel for RNA Analysis Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.es4begw | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Preparation of Denaturing Agarose Gel for RNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.es4begw | 2021-04-15 09:16:57 | ||||
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geneELISA for highthroughput examination of phage?host interactions Resource Report Resource Website |
Matthew Sullivan, Sarah Schwenck, Cristina Howard-Varona, Vinh Dang | DOI:10.17504/protocols.io.dmc42v | VERVE Net, Sullivan Lab | Bacterial viruses (phages) influence global biogeochemical cycles by modulating bacterial mortality, metabolic output and evolution. However, our understanding of phage infections is limited by few methods and environmentally-relevant model systems. Prior work showed that Cellulophaga baltica phage ϕ38:1 infects its original host lytically, and an alternative host either delayed lytically or lysogenically. Here we investigate these infections through traditional and marker-based approaches, and introduce geneELISA for highthroughput examination of phage‒host interactions. | 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 | Matthew Sullivan, Sarah Schwenck, Cristina Howard-Varona, Vinh Dang 2016. geneELISA for highthroughput examination of phage?host interactions. protocols.io https://dx.doi.org/10.17504/protocols.io.dmc42v | 2021-04-15 09:16:57 | |||
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NC64A virus purification Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etebeje | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. NC64A virus purification. protocols.io https://dx.doi.org/10.17504/protocols.io.etebeje | 2021-04-15 09:16:57 | ||||
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Fixing Cells with Paraformaldehyde (PFA) Resource Report Resource Website |
Faculty of Medicine Flow Cytometry Facility, U. of Toronto | DOI:10.17504/protocols.io.c5xy7m | VERVE Net, Sullivan Lab | References:Becton Dickinson Immunocytometry Systems Source Book (1989) 2.10 Lanier, L.L., and Warner, N.L. (1981) Paraformaldehyde Fixation of Hematopoietic Cells for Quantitative Flow Cytometry (FACS) Analysis. Journal of Immunological Methods 47, 25C.A. Williams, M.W. Chase, Stabilizes cell membranes and preserves cell morphology. Methods Immunol. Immunochem. New York 5, (1976) | University of Toronto, University of Toronto | http://www.immunology.utoronto.ca/FlowCytometry/protocols/PFA_Fixation.htm?quot;%3EPreparation%20of%20Paraformaldehyde%20Fixative%3C/a%3E%3Cbr%3E%3C/li%3E%3C/ul%3E%3Ch4%3EExternal%20Protocol%20Links:%3C/h4%3E%3Cul%3E%3Cli%3EPurdue%20University:%C3%82%C2%A0%20%3Ca%20title=PurdueProtocols%20href= | 1 | 2016 | Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Fixing Cells with Paraformaldehyde (PFA). protocols.io https://dx.doi.org/10.17504/protocols.io.c5xy7m | 2021-04-15 09:16:34 | ||
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CviRI Purification From XZ-6E Virus Infected NC64A Chlorella Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.er4bd8w | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.er4bd8w | 2021-04-15 09:16:33 | ||||
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10g/L Fe Stock Solution Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c2zyf5 | VERVE Net, Sullivan Lab | 10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 10g/L Fe Stock Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c2zyf5 | 2021-04-15 09:16:34 | |||
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One-step growth curves for Cellulophaga phages Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.eqfbdtn | VERVE Net, Sullivan Lab | One-step growth curves are used to make determinations about the life cycle of a virus on a particular host. By following a virus infection during one life cycle phase of host a growth curve can be constructed and the burst size can be calculated. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.eqfbdtn | 2021-04-15 09:16:41 | |||
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Phytoplankton and bacteria filtration Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dp55q5 | VERVE Net | For use in "Isolation of cyanophages by liquid bioassays" | 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. Phytoplankton and bacteria filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.dp55q5 | 2021-04-15 09:16:41 | |||
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Chlorella NC64A and Mictractinium Pbi virus Purification Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etfbejn | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Chlorella NC64A and Mictractinium Pbi virus Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.etfbejn | 2021-04-15 09:16:39 | ||||
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CviJI Storage Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esnbede | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Storage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.esnbede | 2021-04-15 09:16:38 | ||||
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Methyltransferase Assay Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etjbekn | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Methyltransferase Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.etjbekn | 2021-04-15 09:16:37 | ||||
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Reconditioning 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.emgbc3w | 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. Reconditioning PCR amplification of the SISPA primer denaturing cycles. protocols.io https://dx.doi.org/10.17504/protocols.io.emgbc3w | 2021-04-15 09:16:59 | |||
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Mock & Technical Protocols for VERVE Net Resource Report Resource Website |
Stanton Burnton, Carolina Cadena, Edmond Dion, Qianwen Luo | DOI:10.17504/protocols.io.etkbekw | VERVE Net | These protocols were developed to show the features of the protocols.io platform and how groups like VERVE Net can implement future protocol design based from the mock and technical protocols written. Each author wrote one specific protocol to model applications of protocols.io and VERVE Net together. | , , , | 1 | 2016 | Stanton Burnton, Carolina Cadena, Edmond Dion, Qianwen Luo 2016. Mock & Technical Protocols for VERVE Net. protocols.io https://dx.doi.org/10.17504/protocols.io.etkbekw | 2021-04-15 09:17:00 | |||
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One Step Procedure for Screening Recombinant Plasmids by Size Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ersbd6e | VERVE Net | University of Nebraska | 1 | 2016 | David Dunigan and Irina Agarkova 2016. One Step Procedure for Screening Recombinant Plasmids by Size. protocols.io https://dx.doi.org/10.17504/protocols.io.ersbd6e | 2021-04-15 09:16:45 | ||||
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Syn33 g20 PCR Resource Report Resource Website |
Marcia Osburne | DOI:10.17504/protocols.io.dai2cd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Marcia Osburne 2016. Syn33 g20 PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dai2cd | 2021-04-15 09:16:45 |
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