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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Mapping Metagenomic Reads to Reference Sequences (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.eyibfue | Sullivan Lab, iVirus | Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter. | The Ohio State University | 2 | 2016 | Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eyibfue | 2021-04-15 09:15:11 | |||
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Soil viral extraction protocol for ssDNA & dsDNA viruses Resource Report Resource Website |
Gary Trubl, Natalie Solonenko | DOI:10.17504/protocols.io.hvxb67n | Sullivan Lab | Protocol for resuspending viruses from soils and sediments. | OSU, OSU | 2 | 2017 | Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.hvxb67n | 2021-04-15 09:15:21 | |||
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Positive and Negative Staining of Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.day2fv | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to negatively or positively stain viruses that have been deposited onto TEM grids so that they can be imaged using transmission electron microscopy (TEM). Positive staining stains the virus itself such that the virus is dark against a lighter background (Figure 1A). This is the easiest staining to do and yields results suitable for analyzing the morphological diversity of viruses from aquatic samples. Negative staining relies on some stain remaining around the edges of a virus such that the details of the virus are clearly defined (Figure 1B). Negative staining is more difficult and is used to obtain publication quality micrographs of viruses.Note: To deposit viruses onto the grids prior to staining, use either the “Adsorbing Viruses onto TEM Grids” protocol or the “Quantitatively Depositing Viruses onto TEM Grids” protocol. Grids should be stained immediately after depositing viruses onto them. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Positive and Negative Staining of Viruses on TEM Grids. protocols.io https://dx.doi.org/10.17504/protocols.io.day2fv | 2021-04-15 09:15:19 | |||
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Analysis of Viral Morphological Characteristics Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dde23d | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to analyze a natural aquatic virus sample using transmission electron microscopy (TEM). The purpose is to obtain the capsid diameter distributions of the viral assemblage, tail length distributions of the viral assemblage, and percentages of each viral morphotype in a sample.Note: Prior to using this protocol, deposit viruses from your sample onto a TEM grid using the protocol “Quantitatively Depositing Viruses onto TEM Grids” then stain the viruses using the protocol “Positive and Negative Staining of Viruses on TEM Grids”. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Analysis of Viral Morphological Characteristics. protocols.io https://dx.doi.org/10.17504/protocols.io.dde23d | 2021-04-15 09:15:29 | |||
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Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging Resource Report Resource Website |
Li Deng, Bonnie T. Poulos, Matthew B. Sullivan | DOI:10.17504/protocols.io.c6zzf5 | VERVE Net, Sullivan Lab | AbstractOcean viruses are abundant, ubiquitous, and play important roles in global biogeochemical cycles through mortality, horizontal gene transfer and manipulation of host metabolism. However, the ability to link viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. Here, we present viral tagging (VT), a method that combines mixtures of isotope labeled host cells and fluorescent viruses with flow cytometry. In a single experiment, we can screen 107 uncultivated ocean viruses with a single strain of Synechococcus. These viruses can then be sequenced to quantitatively link objectivelydefined environmental viral populations, and their genomes, to their hosts. | 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 | Li Deng, Bonnie T. Poulos, Matthew B. Sullivan 2016. Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging. protocols.io https://dx.doi.org/10.17504/protocols.io.c6zzf5 | 2021-04-15 09:15:38 | |||
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Media recipes for Synechococcus isolates Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c9jz4m | VERVE Net, Sullivan Lab | The following are media recipes necessary for isolating and maintaining Synechococcus isolates. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io https://dx.doi.org/10.17504/protocols.io.c9jz4m | 2021-04-15 09:15:09 | |||
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Colony PCR Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c6czav | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Colony PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6czav | 2021-04-15 09:15:39 | ||||
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Preparing Data for vContact from Proteins (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.wigfcbw | 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. | The Ohio State University | https://dx.doi.org/10.7717/peerj.3243 | 4 | 2018 | Benjamin Bolduc 2018. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.wigfcbw | 2021-04-15 09:15:14 | ||
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YTSS Medium Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dbq2mv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. YTSS Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbq2mv | 2021-04-15 09:15:39 | ||||
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SYBR Gold working solutions Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7azid | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold working solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.c7azid | 2021-04-15 09:15:17 | ||||
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Clustering Viral Genomes in iVirus Resource Report Resource Website |
Benjamin Bolduc, Simon Roux | DOI:10.17504/protocols.io.gwebxbe | Sullivan Lab, iVirus | Cluster genomes is script that clusters genomes at a set nucleotide identity and coverage length. Additonally, it offers the ability to cluster sequences whose ends may not align correspondingly, i.e. the special cases of assembled, circular viral genomes that are treated as 'linear' by other sequence-clustering software (that can "miss" the ends).This is 'beta-like' software that has been vetted, though has not been as thoroughly tested as other widely-recognized clustering tools, such as CD-HIT, UCLUST, etc... As with all software, please examine the final results to see if they make sense. | The Ohio State University, The Ohio State University | 1 | 2017 | Benjamin Bolduc, Simon Roux 2017. Clustering Viral Genomes in iVirus. protocols.io https://dx.doi.org/10.17504/protocols.io.gwebxbe | 2021-04-15 09:15:20 | |||
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SYBR Gold Staining for viral enumeration using 13 mm Anodisc 0.02 ?m filters Resource Report Resource Website |
Li Deng & Jennifer Brum | DOI:10.17504/protocols.io.c7cziv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Li Deng & Jennifer Brum 2016. SYBR Gold Staining for viral enumeration using 13 mm Anodisc 0.02 ?m filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c7cziv | 2021-04-15 09:15:49 | ||||
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Large Volume Marine Cyanophage Phage Purification Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3iykd | VERVE Net, Sullivan Lab | Last optimized January 2006, updated by Matt on March 16 2009 | Matthew Sullivan | 1 | 2016 | Matthew Sullivan 2016. Large Volume Marine Cyanophage Phage Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3iykd | 2021-04-15 09:15:49 | |||
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FISH Protocol for FISH & FLOW Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfe3jd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. FISH Protocol for FISH & FLOW. protocols.io https://dx.doi.org/10.17504/protocols.io.dfe3jd | 2021-04-15 09:15:30 | ||||
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Cesium Chloride Gradients Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7dzi5 | VERVE Net, Sullivan Lab | The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for Viruses (See guidelines for DNA Extraction). | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Cesium Chloride Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.c7dzi5 | 2021-04-15 09:15:30 | |||
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Identifying Viral Sequences Using VirSorter (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ev2be8e | Sullivan Lab | 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: 10.1038/ismej.2016.89 | The Ohio State University | https://doi.org/ismej201689 | 1 | 2016 | Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ev2be8e | 2021-04-15 09:15:33 | |
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Centrifuged Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddj24m | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddj24m | 2021-04-15 09:15:35 | |||
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Low input Library Preparation for Illumina Sequencing Resource Report Resource Website |
Adriana Alberti | DOI:10.17504/protocols.io.ddq25v | VERVE Net, Sullivan Lab | Protocol for preparation of short single and paired-end libraries from genomic dsDNA starting from low DNA quantity (up to 10 ng) for Illumina sequenincg. Developed by Adriana Alberti at Genoscope. | Teytelman L, Stoliartchouk A, Kindler L, Hurwitz BL, Protocols.io: Virtual Communities for Protocol Development and Discussion. PLoS Biology 14(8). doi: 10.1371/journal.pbio.1002538 | Matthew Sullivan Lab | https://doi.org/10.1371/journal.pbio.1002538 | 1 | 2016 | Adriana Alberti 2016. Low input Library Preparation for Illumina Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.ddq25v | 2021-04-15 09:15:35 | |
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Host Range Protocols Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dew3fd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Host Range Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.dew3fd | 2021-04-15 09:15:36 | ||||
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Working Bead Solution Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c84zyv | VERVE Net, Sullivan Lab | For use in Wet-mount Method for Enumeration of Aquatic Viruses | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Working Bead Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c84zyv | 2021-04-15 09:15:39 |
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