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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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1M Tris Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5vy65 | VERVE Net, Sullivan Lab | This shows how to make 1M Tris. | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. 1M Tris. protocols.io https://dx.doi.org/10.17504/protocols.io.c5vy65 | 2021-04-15 09:16:19 | |||
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g20 (myovirus) PCR Protocol Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.dam2c5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Li Deng 2016. g20 (myovirus) PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dam2c5 | 2021-04-15 09:16:19 | ||||
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Marine Basal Media Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dcc2sv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Marine Basal Media. protocols.io https://dx.doi.org/10.17504/protocols.io.dcc2sv | 2021-04-15 09:16:37 | ||||
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Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek3bcyn | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ek3bcyn | 2021-04-15 09:16:21 | |||
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16S Universal Bacterial PCR Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfr3m5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dfr3m5 | 2021-04-15 09:16:25 | ||||
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Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ev8be9w | Sullivan Lab | A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure. | Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB, iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal 11(1). doi: 10.1038/ismej.2016.89 | The Ohio State University | https://dx.doi.org/10.1038/ismej.2016.89 | 1 | 2016 | Benjamin Bolduc 2016. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ev8be9w | 2021-04-15 09:16:44 | |
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Cesium Chloride Dialysis for Viruses Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7jzkm | VERVE Net, Sullivan Lab | Version 3This protocol describes the use of Cesium Chloride to purify viruses with an optional dialysis step to remove the CsCl. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012.References:Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 15(5), 1428–1440. doi:10.1111/j.1462-2920.2012.02836.x. | University of Arizona, Ohio State University | http://www.eebweb.arizona.edu/faculty/mbsulli/protocols/protocols/CsCl_Virus_Purification_Dialysis_v3.pdf | 1 | 2016 | Matthew Sullivan 2016. Cesium Chloride Dialysis for Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.c7jzkm | 2021-04-15 09:16:52 | ||
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Microbubbling technique Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.egkbbuw | VERVE Net, Sullivan Lab | For use in the protocol "Large Volume Marine Cyanophage protocols" | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Microbubbling technique. protocols.io https://dx.doi.org/10.17504/protocols.io.egkbbuw | 2021-04-15 09:16:27 | |||
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Adsorbing Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dar2d5 | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with high concentrations of viruses. For natural samples, use the protocol “Quantitatively Depositing Viruses onto TEM Grids using an Airfuge”.Note: If purification of the viruses is necessary, refer to Ackermann and Heldal (2010) for various options. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Adsorbing Viruses on TEM Grids. protocols.io https://dx.doi.org/10.17504/protocols.io.dar2d5 | 2021-04-15 09:16:51 | |||
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SYBR Gold Staining for Viral Enumeration (Case 2) Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7fzjm | VERVE Net, Sullivan Lab | Case 2: Fix samples. Use this protocol when long term storage of slide is required.For when you can count your samples in a few days, see Case 1. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 2). protocols.io https://dx.doi.org/10.17504/protocols.io.c7fzjm | 2021-04-15 09:16:50 | |||
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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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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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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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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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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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