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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Checking DNA Concentration with Agarose Gel Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c35yq5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Checking DNA Concentration with Agarose Gel. protocols.io https://dx.doi.org/10.17504/protocols.io.c35yq5 | 2021-04-15 09:14:32 | ||||
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MetaPhlAn profiling of 20 HMP samples Resource Report Resource Website |
Curtis Huttenhower | DOI:10.17504/protocols.io.d9e93d | VERVE Net, Huttenhower Lab | In this protocol we will show how to taxonomically profile 20 metagenomic shotgun samples Human Microbiome Project (HMP). Specifically, we will look at 10 samples from the buccal mucosa and 10 from the tongue dorsum. Please note these 20 samples are not necessarily an unbiased selection of microbiomes from the over 200 buccal mucosa and tongue dorsum samples generated by the HMP.REQUIREMENTS: BowTie2 installed and in the system path, Mercurial, basic unix commands (wget, tar).The size of the 20 samples (60GBs) can make their download quite slow. For this reason we are also providing the overall output of this protocol (few KBs) available for download so that one can start the tutorial from MetaPhlAn output merge and visualization if needed. | https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial | 1 | 2016 | Curtis Huttenhower 2016. MetaPhlAn profiling of 20 HMP samples. protocols.io https://dx.doi.org/10.17504/protocols.io.d9e93d | 2021-04-15 09:14:43 | |||
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30.0% Acrylamide stock solution (30.0:0.8) Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eq2bdye | VERVE Net | For use in Polyacrylamide Gel System For Electrophoresis Of Proteins. | 1 | 2016 | David Dunigan and Irina Agarkova 2016. 30.0% Acrylamide stock solution (30.0:0.8). protocols.io https://dx.doi.org/10.17504/protocols.io.eq2bdye | 2021-04-15 09:14:32 | ||||
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Purification of viral assemblages from seawater in CsCl gradients Resource Report Resource Website |
Janice E. Lawrence and Grieg F. Steward | DOI:10.17504/protocols.io.d2s8ed | VERVE Net | OptiPrep gradients, as described for purifying viral isolates, may also be used for purifying marine viral assemblages. There are as yet, however, few descriptions of this application in the literature. CsCl gradients, on the other hand, have been used extensively for purifications of viral isolates and natural viral assemblages. Given the continued popularity of CsCl gradients, and their well-characterized performance, we present the following two-part purification and fractionation protocol for viruses in CsCl gradients. The first part involves relatively quick sedimentation through a step-gradient to remove the bulk of the contaminants. This is followed by a higher resolution continuous gradient to separate the viruses from residual contaminants and to separate viruses having differing buoyant densities from one another. We assume the starting material for the following procedure to be a concentrated suspension of viruses (whether filtered to remove cells or not). | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_166.pdf | 1 | 2015 | Janice E. Lawrence and Grieg F. Steward 2015. Purification of viral assemblages from seawater in CsCl gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.d2s8ed | 2021-04-15 09:14:33 | ||
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VBRC Base By Base: Export an image of the alignment Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecnbave | VERVE Net, Upton-Lab | Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Export an image of the alignment. protocols.io https://dx.doi.org/10.17504/protocols.io.ecnbave | 2021-04-15 09:14:43 | ||
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Most Probable Number (MPN) Counts of Cyanophages Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ddb22m | VERVE Net, Sullivan Lab | Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Most Probable Number (MPN) Counts of Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddb22m | 2021-04-15 09:14:51 | |||
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Generating viral metagenomes from the coral holobiont 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.ejgbcjw | VERVE Net | Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis. | , , , | http://journal.frontiersin.org/article/10.3389/fmicb.2014.00206/full | 1 | 2016 | Karen D. Weynberg, Elisha M. Wood-Charlson, Curtis A. Suttle, and Madeleine J. H. van Oppen 2016. Generating viral metagenomes from the coral holobiont. protocols.io https://dx.doi.org/10.17504/protocols.io.ejgbcjw | 2021-04-15 09:14:49 | ||
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Enumerating algal viruses by flow cytometry Resource Report Resource Website |
Amy Zimmerman, Camille Poirier | DOI:10.17504/protocols.io.guibwue | VERVE Net, Worden Lab | Purpose: To quantify virus-like particles in culture or environmental samples.Host cells and virus-like particles are enumerated from the same glutaraldehyde-fixed sample. For virus counts, an aliquot is diluted in 0.02-µm-filtered TE buffer prior to staining with SYBR Green I nucleic acid dye to improve staining efficiency and ensure an appropriately low event rate in the instrument. An unstained aliquot of sample is run for host cell counts. | Worden Lab, Monterey Bay Aquarium Research Institute, Worden Lab, Monterey Bay Aquarium Research Institute | 2 | 2017 | Amy Zimmerman, Camille Poirier 2017. Enumerating algal viruses by flow cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.guibwue | 2021-04-15 09:14:50 | |||
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CviJI Assay Conditions Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esqbedw | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Assay Conditions. protocols.io https://dx.doi.org/10.17504/protocols.io.esqbedw | 2021-04-15 09:14:36 | ||||
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RNA Samples Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dev3e5 | 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. RNA Samples Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.dev3e5 | 2021-04-15 09:14:34 | |||
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Polyacrylamide Gel System For Electrophoresis Of Proteins Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ep7bdrn | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Polyacrylamide Gel System For Electrophoresis Of Proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.ep7bdrn | 2021-04-15 09:14:53 | ||||
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Ascorbic Acid Antifade Solution Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c87zzm | VERVE Net, Sullivan Lab | For use in 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. Ascorbic Acid Antifade Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c87zzm | 2021-04-15 09:14:56 | |||
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EGTA tetrasodium salt Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3pymm | VERVE Net, Sullivan Lab | For use in DNase I Treatment protocol for DNase inactivation | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Matthew Sullivan 2015. EGTA tetrasodium salt. protocols.io https://dx.doi.org/10.17504/protocols.io.c3pymm | 2021-04-15 09:14:39 | |||
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Script R8: Plotting Bacterial Taxonomy from MetaPhlan Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejbbcin | VERVE Net, Club Grice | This protocol outlines the analysis used to plot MetaPhlAn taxonomic assignments. Based on methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R8: Plotting Bacterial Taxonomy from MetaPhlan. protocols.io https://dx.doi.org/10.17504/protocols.io.ejbbcin | 2021-04-15 09:14:59 | |
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Viral and bacterial isolates, propagation and preparation of stocks Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | DOI:10.17504/protocols.io.dzs76d | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | The following procedure is an adaptation of the original FLVP protocol from Hennes et al. (1995) for use with SYBR Green I stain. Normally, this protocol will take 2 days given that the softening of the viral pellet is an overnight step. However, if the viral pellet redissolves quickly, it can be accomplished in 1 day. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_019.pdf | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. Viral and bacterial isolates, propagation and preparation of stocks. protocols.io https://dx.doi.org/10.17504/protocols.io.dzs76d | 2021-04-15 09:15:05 | ||
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MTN100 with 1x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.def3bm | VERVE Net, Sullivan Lab | This mixture is is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 1x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.def3bm | 2021-04-15 09:14:44 | |||
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Script P10: CRISPR Identification Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ehdbb26 | VERVE Net, Club Grice | This protocol provides a method for identifing CRIPR repeats using the program PilerCR on assembled contigs. Based on the methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P10: CRISPR Identification. protocols.io https://dx.doi.org/10.17504/protocols.io.ehdbb26 | 2021-04-15 09:14:44 | |
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Preparing target indicator cells Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqi5ud | VERVE Net | For use in "Isolation of cyanophages by plaque assays" | Manual of Aquatic Virology, Manual of Aquatic Virology, Manual of Aquatic Virology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Preparing target indicator cells. protocols.io https://dx.doi.org/10.17504/protocols.io.dqi5ud | 2021-04-15 09:14:44 | |||
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Purifying Viruses Using Sucrose Cushion Resource Report Resource Website |
Shannon Williamson | DOI:10.17504/protocols.io.c3wypd | VERVE Net, Sullivan Lab | This protocol describes the use of a sucrose cushion to purify viruses. It is the Matthew Sullivan Lab adaptation of the Shannon Williamson protocol.DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012.Citation: 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. Environmental Microbiology. doi:10.1111/j.1462-2920.2012.02836.x | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Shannon Williamson 2015. Purifying Viruses Using Sucrose Cushion. protocols.io https://dx.doi.org/10.17504/protocols.io.c3wypd | 2021-04-15 09:15:13 | |||
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Screening Recombinant Clones by PCR Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c48yzv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Screening Recombinant Clones by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.c48yzv | 2021-04-15 09:14:49 |
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