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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Adsorbing Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | 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 dx.doi.org/10.17504/protocols.io.dar2d5 | 2021-03-29 03:10:39 | |||
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Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Bonnie Poulos | 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 dx.doi.org/10.17504/protocols.io.ek4bcyw | 2021-03-29 03:10:34 | ||||
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SYBR Gold Staining for Viral Enumeration (Case 2) Resource Report Resource Website |
Li Deng | 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 dx.doi.org/10.17504/protocols.io.c7fzjm | 2021-03-29 03:10:35 | |||
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Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Matthew Sullivan | 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 dx.doi.org/10.17504/protocols.io.dep3dm | 2021-03-29 03:10:51 | |||
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Titration of AmPure XP Beads for Removal of Fragments Resource Report Resource Website |
Matthew Sullivan | 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 dx.doi.org/10.17504/protocols.io.c52y8d | 2021-03-29 03:10:45 | ||||
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Cellulophaga growth reading Resource Report Resource Website |
Matthew Sullivan | 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 dx.doi.org/10.17504/protocols.io.dpa5id | 2021-03-29 03:10:55 | |||
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10g/L Fe Stock Solution Resource Report Resource Website |
Matthew Sullivan Lab | 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 dx.doi.org/10.17504/protocols.io.c2zyf5 | 2021-03-29 03:11:04 | |||
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RNAlater Recipe Resource Report Resource Website |
Rex Malmstrom | 10.17504/protocols.io.c56y9d | VERVE Net, Sullivan Lab | This is a storage solution that stabilizes and protectsRNA while inactivating RNase | MIT/Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Rex Malmstrom 2015. RNAlater Recipe. protocols.io dx.doi.org/10.17504/protocols.io.c56y9d | 2021-03-29 03:09:29 | |||
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CsCl Step Gradient Buffer Resource Report Resource Website |
Jonathan King | 10.17504/protocols.io.dmj44m | VERVE Net, Sullivan Lab | This mixture is used in the CsCl Step Gradient to Purify Phage Protocol | King Lab, MIT | http://web.mit.edu/king-lab/www/cookbook/cscl_grad_phage.htm | 1 | 2016 | Jonathan King 2016. CsCl Step Gradient Buffer. protocols.io dx.doi.org/10.17504/protocols.io.dmj44m | 2021-03-29 03:09:36 | ||
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Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | 10.17504/protocols.io.x5xfq7n | VERVE Net, Sullivan Lab, iVirus | 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. | The Ohio State University | https://doi.org/10.1101/533240 | 5 | 2019 | Benjamin Bolduc 2019. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.x5xfq7n | 2021-03-29 03:09:41 | ||
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Wet-mount Method for Enumeration of Aquatic Viruses Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | 10.17504/protocols.io.c8pzvm | VERVE Net, Sullivan Lab | Purpose: This method for the enumeration of aquatic viruses is a low-cost alternative to the commonly used filter-mount method. Briefly, fluorescently-stained samples are wetmounted directly onto slides for epifluorescence microscopy after an optional chemical flocculation concentration step used for samples with anticipated virus concentrations of 7 viruses mL-1 (samples with >5×107 viruses mL-1 do not require this concentration step prior to analysis). Virus concentration in the wet-mounted sample is determined from the ratio of viruses to microsphere beads, which are added at a known concentration. This wet-mount method for enumerating viruses is significantly less expensive than the filter-mount method (i.e., the cost of microsphere beads per sample is ~500-fold lower than the cost of one filter per sample), and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations encountered in field and laboratory samples. The only limitation of this method is that samples with virus concentrations ≤1×106 viruses mL-1 cannot be enumerated, as the abundance of viruses is too low for efficient enumeration.Figure 1. Overview of the 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. Wet-mount Method for Enumeration of Aquatic Viruses. protocols.io dx.doi.org/10.17504/protocols.io.c8pzvm | 2021-03-29 03:09:37 | |||
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Pseudoalteromonas Media Recipes Resource Report Resource Website |
Natalie Solonenko | 10.17504/protocols.io.fz4bp8w | Sullivan Lab | Now includes media used for phosphate limitation experiments. | OSU | 1 | 2016 | Natalie Solonenko 2016. Pseudoalteromonas Media Recipes. protocols.io dx.doi.org/10.17504/protocols.io.fz4bp8w | 2021-03-29 03:09:37 | |||
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0.5M NH4Cl Resource Report Resource Website |
Matthew Sullivan Lab | 10.17504/protocols.io.c77zrm | 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. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm | 2021-03-29 03:09:44 | |||
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1M Tris Resource Report Resource Website |
Ms Alex Aitken | 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 dx.doi.org/10.17504/protocols.io.c5vy65 | 2021-03-29 03:09:59 | |||
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DNA extraction for HMW DNA Resource Report Resource Website |
Natalie Solonenko, Marie Burris | 10.17504/protocols.io.6cbhasn | Sullivan Lab, Temperton Lab | This protocol is intended for extraction of HMW DNA from bacterial or viral samples. | The Ohio State University Department of Microbiology, The Ohio State University Department of Microbiology | 1 | 2019 | Natalie Solonenko, Marie Burris 2019. DNA extraction for HMW DNA. protocols.io dx.doi.org/10.17504/protocols.io.6cbhasn | 2021-03-29 03:10:11 | |||
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Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | 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 dx.doi.org/10.17504/protocols.io.ev8be9w | 2021-03-29 03:10:25 | |
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16S Universal Bacterial PCR Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.dfr3m5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io dx.doi.org/10.17504/protocols.io.dfr3m5 | 2021-03-29 03:10:29 | ||||
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Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Matthew Sullivan | 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 dx.doi.org/10.17504/protocols.io.dem3c5 | 2021-03-29 03:10:30 | ||||
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DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns Resource Report Resource Website |
Marine Phage Lab, Matthew Sullivan Lab | 10.17504/protocols.io.c26yhd | VERVE Net, Sullivan Lab | Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega. | Matthew Sullivan Lab, University of Arizona, Ohio State University, Matthew Sullivan Lab, University of Arizona, Ohio State University | http://www.eebweb.arizona.edu/faculty/mbsulli/protocols/protocols/Wizard_Column_Viral_DNA_Extraction_v1.pdf | 1 | 2016 | Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io dx.doi.org/10.17504/protocols.io.c26yhd | 2021-03-29 03:08:44 | ||
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Identifying Viral Sequences Using VirSorter (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | 10.17504/protocols.io.eyjbfun | Sullivan Lab, iVirus | Identifying putative viral sequences from SPAdes-assembled data from the Ocean Sampling Day (2014) metagenomic datasets using VirSorter. | 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: ismej201689 | The Ohio State University | https://www.nature.com/articles/ismej201689.pdf?origin=ppub | 2 | 2016 | Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.eyjbfun | 2021-03-29 03:08:28 |
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