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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Identifying Viral Sequences Using VirSorter (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI: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 https://dx.doi.org/10.17504/protocols.io.eyjbfun | 2021-04-15 09:15:41 | |
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TE Buffer Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5uy6v | VERVE Net, Sullivan Lab | TE is a commonly used buffer solution in molecular biology, especially in procedures involving DNA or RNA. "TE" is derived from its components: Tris, a common pH buffer, and EDTA, a molecule that chelates cations like Mg2+. The purpose of TE buffer is to solubilize DNA or RNA, while protecting it from degradation: 10 mM Tris, bring to pH 8.0 with HCl, 1 mM EDTA | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. TE Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5uy6v | 2021-04-15 09:15:46 | |||
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phageFISH Protocol Resource Report Resource Website |
Cristina Moraru & Elke Allers | DOI:10.17504/protocols.io.c9iz4d | VERVE Net, Sullivan Lab | This protocol combines phage gene detection with rRNA detection for the identification of host cells and detection of free phage particles. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Cristina Moraru & Elke Allers 2016. phageFISH Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c9iz4d | 2021-04-15 09:15:57 | |||
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Quality Control of Reads Using Trimmomatic (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.gvybw7w | 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.Quality trimming of reads is important! | The Ohio State University | 1 | 2016 | Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gvybw7w | 2021-04-15 09:15:58 | |||
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Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.c54y8v | VERVE Net, Sullivan Lab | This protocol describes how to concentrate viruses in liquid samples using an Amicon or Nanosep centrifugal ultrafiltration device. We use Amicons to concentrate medium volumes of samples (10s to 100s of mls) down to a final volume of ~4 ml. We use Nanoseps to concentrate smaller volumes of sample ( | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device. protocols.io https://dx.doi.org/10.17504/protocols.io.c54y8v | 2021-04-15 09:16:02 | |||
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Lysis Buffer (20 mL) Resource Report Resource Website |
Matt Sullivan Lab | DOI:10.17504/protocols.io.c4gytv | VERVE Net, Sullivan Lab | Must be made fresh before experiment because of the Sucrose. For 20 mL solutions. | Matt Sullivan Lab | 1 | 2017 | Matt Sullivan Lab 2017. Lysis Buffer (20 mL). protocols.io https://dx.doi.org/10.17504/protocols.io.c4gytv | 2021-04-15 09:16:04 | |||
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Can Crusher-Culley Protocol Resource Report Resource Website |
Alexander Culley, Grieg Steward | DOI:10.17504/protocols.io.c3jykm | VERVE Net, Sullivan Lab | Culley Protocol (from Culley & Steward (2007), New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences, Applied & Environmental Microbiology 73(18):5937-5944). | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Alexander Culley, Grieg Steward 2015. Can Crusher-Culley Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c3jykm | 2021-04-15 09:16:08 | |||
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SYBR Gold Staining for Viral Enumeration (Case 1) Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c69zh5 | VERVE Net, Sullivan Lab | Case 1: Quick check of viral concentration. Use this protocol when you can count your samples in a few days.For when long term storage of slide is required, see Case 2. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 1). protocols.io https://dx.doi.org/10.17504/protocols.io.c69zh5 | 2021-04-15 09:16:08 | |||
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Viral sequence identification SOP with VirSorter2 Resource Report Resource Website |
Jiarong Guo, Dean Vik, Akbar Adjie Pratama, Simon Roux, Matthew Sullivan | DOI:10.17504/protocols.io.btv8nn9w | Sullivan Lab, iVirus | This protocol shows how to use VirSorter2, checkV, DRAMv and some manual curation criteria for viral sequence identification. | Ohio State University, Columbus, Ohio State University, Columbus, Ohio State University, Columbus, LBNL, DOE Joint Genome Institute, Ohio State University, Columbus | 2 | 2021 | Jiarong Guo, Dean Vik, Akbar Adjie Pratama, Simon Roux, Matthew Sullivan 2021. Viral sequence identification SOP with VirSorter2. protocols.io https://dx.doi.org/10.17504/protocols.io.btv8nn9w | 2021-04-15 09:16:09 | |||
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Treatments and Preservation of Seawater Samples for FISH Resource Report Resource Website |
Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer | DOI:10.17504/protocols.io.c5by2m | VERVE Net, Sullivan Lab | This protocol gives a method for treatment and preservation of seawater samples that will be subject to fluorescence in situ hybridization (FISH). Samples are used with fluorescent probes to determine what populations of bacteria or other microbes are present. The filters may also be used to simply count the number of microbes in a sample. Requires varying amounts of 10µm or 200µm filtrate (up to 11.5L for open ocean depth profile) as shown in Table I. | 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 | 2015 | Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer 2015. Treatments and Preservation of Seawater Samples for FISH. protocols.io https://dx.doi.org/10.17504/protocols.io.c5by2m | 2021-04-15 09:16:11 | |||
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NATURAL SEAWATER-BASED PRO99 MEDIUM Resource Report Resource Website |
Chisholm Lab | DOI:10.17504/protocols.io.c7zzp5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Chisholm Lab 2016. NATURAL SEAWATER-BASED PRO99 MEDIUM. protocols.io https://dx.doi.org/10.17504/protocols.io.c7zzp5 | 2021-04-15 09:16:10 | ||||
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Preparing Data for vContact from Proteins (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.gwdbxa6 | Sullivan Lab, iVirus | Preparing data for use in vContact by using VirSorted Ocean Sampling Day (2014) contigs, using tools available in Cyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this protocol are suitable for vContact-PCs. | Bolduc B, Jang HB, Doulcier G, You Z, Roux S, Sullivan MB, vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect and . PeerJ doi: 10.7717/peerj.3243 | The Ohio State University | https://dx.doi.org/10.7717/peerj.3243 | 3 | 2017 | Benjamin Bolduc 2017. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gwdbxa6 | 2021-04-15 09:16:12 | |
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Plating Prochlorococcus and Synechococcus strains in top agarose for plaque assays Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3vyn5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Plating Prochlorococcus and Synechococcus strains in top agarose for plaque assays. protocols.io https://dx.doi.org/10.17504/protocols.io.c3vyn5 | 2021-04-15 09:16:14 | ||||
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16s Pyrotag PCR Resource Report Resource Website |
Howard Ochman | DOI:10.17504/protocols.io.c5iy4d | VERVE Net, Sullivan Lab | Modified from H. Ochman protocol: Environ. Micro. 2009 Kunin, Engelbrekson Ochman & Hugenholtz | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Howard Ochman 2016. 16s Pyrotag PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.c5iy4d | 2021-04-15 09:16:12 | |||
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Treatments for the Preservation of Seawater Samples Resource Report Resource Website |
Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer | DOI:10.17504/protocols.io.c29yh5 | VERVE Net, Sullivan Lab | This protocol consists of several methods for the preservation of seawater samples to later perform various techniques in the lab. It is meant as a sampling treatment in the field and is written as comprehensive; however, depending on needs and scientific questions, any or all of the methods may be used.Flow Cytometry (FCM): Samples are used for counting bacteria and for sorting different groups of microbes (eg, sorting synechococcus and prochlorococcus and non-fluorescent bacteria). Glutaraldehyde fixes microbes and renders them unculturable whereas microbes preserved in DMSO and Betaine can usually be cultured after thawing and rinsing. Betaine was developed for single cell sorting and may be a better preservative than DMSO.SYBR staining: Samples are used for counting bacteria (unfiltered or pre-filtered seawater) and viruses (unfiltered, pre-filtered or 0.2um filtered seawater) microscopically after staining with SYBR-Gold (or SYBR-Green). Transmission Electron Microscopy (TEM): Samples are used for determining frequency of visibly infected cells (FVIC) and determining types of microbes or viruses present, and can be quantitative.Quantitative PCR (qPCR): Samples are used for quantitative PCR of microbes. They can also be used for quantitative PCR of viruses.Viral qPCR: Samples are used for quantitative PCR of viruses.Culturing Viruses: Samples are used for cultivating viruses by solid or liquid plaque assay on susceptible hosts. Samples can also be used for viral tagging (using flow cytometry) and most probable number (MPN) assays.Fluorescence in situ hybridization (FISH): Samples are used with fluorescent probes to determine what populations of bacteria or other microbes are present. The filters may also be used to simply count the number of microbes in a sample. For detailed FISH procedure see here. | 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 | 2015 | Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer 2015. Treatments for the Preservation of Seawater Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.c29yh5 | 2021-04-15 09:16:19 | |||
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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.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 https://dx.doi.org/10.17504/protocols.io.x5xfq7n | 2021-04-15 09:16:25 | ||
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CsCl Step Gradient Buffer Resource Report Resource Website |
Jonathan King | DOI: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 https://dx.doi.org/10.17504/protocols.io.dmj44m | 2021-04-15 09:16:14 | ||
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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 | DOI: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 https://dx.doi.org/10.17504/protocols.io.c8pzvm | 2021-04-15 09:16:22 | |||
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1M Citrate and Magnesium Resuspension Buffer Resource Report Resource Website |
Lauren Chittick | DOI:10.17504/protocols.io.exybfpw | Sullivan Lab | 1 | 2016 | Lauren Chittick 2016. 1M Citrate and Magnesium Resuspension Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.exybfpw | 2021-04-15 09:16:17 | |||||
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Protocol for SYBR Counts of Cyanophages and Bacteria Resource Report Resource Website |
Ross Fu and Matt Sullivan | DOI:10.17504/protocols.io.c7wzpd | VERVE Net, Sullivan Lab | Purpose: to determine the concentration of DNA-containing particles in a given sample; useful in finding cell counts or phage titers. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Ross Fu and Matt Sullivan 2016. Protocol for SYBR Counts of Cyanophages and Bacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.c7wzpd | 2021-04-15 09:16:30 |
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