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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Preparation of reagents Resource Report Resource Website |
Curtis A. Suttle and Jed A. Fuhrman | DOI:10.17504/protocols.io.dqj5um | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | For Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy protocol. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_145.pdf | 1 | 2015 | Curtis A. Suttle and Jed A. Fuhrman 2015. Preparation of reagents. protocols.io https://dx.doi.org/10.17504/protocols.io.dqj5um | 2021-04-15 09:16:37 | ||
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Plate Amplification Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dq75zm | VERVE Net | For use in "Obtaining pure cyanophage stock: plaque purification" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Plate Amplification. protocols.io https://dx.doi.org/10.17504/protocols.io.dq75zm | 2021-04-15 09:16:59 | |||
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Sample collection and preparation Resource Report Resource Website |
Curtis A. Suttle and Jed A. Fuhrman | DOI:10.17504/protocols.io.dqk5uv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | For Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy protocol. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_145.pdf | 1 | 2015 | Curtis A. Suttle and Jed A. Fuhrman 2015. Sample collection and preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.dqk5uv | 2021-04-15 09:16:42 | ||
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Script R10: Whole Metagenome Beta Diversity Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejebcje | VERVE Net, Club Grice | This protocol outlines the beta-diversity analysis that we performed on the whole metagenome samples. We measured the signifiance of the dissimilarity between samples that were grouped by biological occlusion status, microenvironment (sebaceous, moist, etc), and sampling time point. Here we also describe our intrapersonal vs interpersonal dissimilarity measurements. 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 R10: Whole Metagenome Beta Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.ejebcje | 2021-04-15 09:17:00 | |
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CsCl Step Gradient to Purify Phage Resource Report Resource Website |
Jonathan King Lab | DOI:10.17504/protocols.io.c4zyx5 | VERVE Net, Sullivan Lab | April 2000 chpPhage are best purified by a CsCl gradient. This is separated by density not sedimentation as in a sucrose gradient.This is a protocol for P22 like phage not T4 with delicate tail fibers. | Jonathan King Lab, MIT | http://web.mit.edu/king-lab/www/cookbook/cscl_grad_phage.htm | 1 | 2016 | Jonathan King Lab 2016. CsCl Step Gradient to Purify Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c4zyx5 | 2021-04-15 09:16:45 | ||
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VBRC Base By Base: Export a text overview of the alignment Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecmbau6 | 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 a text overview of the alignment. protocols.io https://dx.doi.org/10.17504/protocols.io.ecmbau6 | 2021-04-15 09:16:59 | ||
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Artificial Seawater Based AMP1 Medium Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.c9mz45 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Artificial Seawater Based AMP1 Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.c9mz45 | 2021-04-15 09:16:48 | ||||
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Cesium Chloride Protocol for Phage Resource Report Resource Website |
Forest Rohwer | DOI:10.17504/protocols.io.c37yrm | VERVE Net, Sullivan Lab | This protocol contains 4 sections: 1. Cesium Chloride Gradient to separate phage from bacteria. Marine viruses around 1.5g/ml 2. DNase I treatment of CsCl-purified phage 3. Formamide Extraction of DNA from phagE4. 4. CTAB | Matthew Sullivan Lab | 1 | 2016 | Forest Rohwer 2016. Cesium Chloride Protocol for Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c37yrm | 2021-04-15 09:17:01 | |||
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Media Recipes Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.deq3dv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.deq3dv | 2021-04-15 09:16:49 | ||||
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Marine Purity Broth Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ekrbcv6 | VERVE Net, Sullivan Lab | Purpose: To test axenic cultures for purity. Protocol described in S. Bertillson, O. Berglund, D.M. Karl, S.W. Chisholm (2003). Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea. Limnol Oceanogr 48(5):1721-1731. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.ekrbcv6 | 2021-04-15 09:17:02 | |||
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Simultaneous measurement of grazing and viral lysis of phytoplankton Resource Report Resource Website |
Corina Brussaard, Anne-Claire Baudoux, Anna A. M. Noordeloos, Marcel J. W. Veldhuis | DOI:10.17504/protocols.io.dyb7sm | VERVE Net | An alternate version to the protocol "Simultaneous measurement of grazing and viral lysis of phytoplankton v1" | Royal Netherlands Institute for Sea Research, Royal Netherlands Institute for Sea Research, Royal Netherlands Institute for Sea Research, Royal Netherlands Institute for Sea Research | 2 | 2016 | Corina Brussaard, Anne-Claire Baudoux, Anna A. M. Noordeloos, Marcel J. W. Veldhuis 2016. Simultaneous measurement of grazing and viral lysis of phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.dyb7sm | 2021-04-15 09:16:51 | |||
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Isolation from Lysogens Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.ebdbai6 | VERVE Net | This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_057.pdf | 1 | 2016 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Isolation from Lysogens. protocols.io https://dx.doi.org/10.17504/protocols.io.ebdbai6 | 2021-04-15 09:17:01 | ||
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Filter drying procedure Resource Report Resource Website |
Jed Fuhrman | DOI:10.17504/protocols.io.dju4nv | VERVE Net, Fuhrman Lab | For use in "SYBR Green Assay". | Hurwitz Lab | 1 | 2015 | Jed Fuhrman 2015. Filter drying procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.dju4nv | 2021-04-15 09:16:48 | |||
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Purification of viruses via CsCl gradient and ultracentrifugation Resource Report Resource Website |
Jozef Nissimov | DOI:10.17504/protocols.io.d9k94v | VERVE Net, Bidle Lab | Purification of viruses via CsCl gradient and ultracentrifugation | DMCS, Rutgers University | 1 | 2015 | Jozef Nissimov 2015. Purification of viruses via CsCl gradient and ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.d9k94v | 2021-04-15 09:17:04 | |||
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Non-Centrifuged Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddk24v | 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. Non-Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddk24v | 2021-04-15 09:17:04 | |||
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Metabolic profiling with HUMAnN Resource Report Resource Website |
Curtis Huttenhower | DOI:10.17504/protocols.io.d9799m | VERVE Net, Huttenhower Lab | In this protocol, we perform a metabolic profiling of metagenomic datasets using HUMAnN applied to the 20 samples taxonomically profiled in the other protocols contained in this collection.Once the metabolic profile has been generated, the following protocols can be performed:MetaPhlAn output merge and visualizationsGraPhlAn visualization of single and multiple samplesTaxonomic biomarker discovery with LEfSe | https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial | 1 | 2016 | Curtis Huttenhower 2016. Metabolic profiling with HUMAnN. protocols.io https://dx.doi.org/10.17504/protocols.io.d9799m | 2021-04-15 09:17:00 | |||
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Running VirSorter in iPlant Discovery Environment Resource Report Resource Website |
Simon Roux, Francois Enault, Bonnie L. Hurwitz, Matthew B. Sullivan | DOI:10.17504/protocols.io.d8u9wv | VERVE Net, Hurwitz Lab, Plantae | This protocol gives an introduction to running VirSorter in the iPlant Discovery Environment. | University of Arizona, University of Arizona, University of Arizona, University of Arizona | https://peerj.com/articles/985/ | 1 | 2016 | Simon Roux, Francois Enault, Bonnie L. Hurwitz, Matthew B. Sullivan 2016. Running VirSorter in iPlant Discovery Environment. protocols.io https://dx.doi.org/10.17504/protocols.io.d8u9wv | 2021-04-15 09:16:59 | ||
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CviRI Assay Conditions Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.es3begn | VERVE Net | For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Assay Conditions. protocols.io https://dx.doi.org/10.17504/protocols.io.es3begn | 2021-04-15 09:17:04 | ||||
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Using ImageJ to Measure Viral Dimensions in Micrographs Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.ddf23m | VERVE Net, Sullivan Lab | Purpose: This protocol describes the use of ImageJ to measure dimensions of viruses in TEM micrographs, but can be applied to the measurement of anything in any image. The ImageJ program can be downloaded free (http://rsbweb.nih.gov/ij/) and it’s usage should be cited in publications using the reference listed on the website. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Using ImageJ to Measure Viral Dimensions in Micrographs. protocols.io https://dx.doi.org/10.17504/protocols.io.ddf23m | 2021-04-15 09:17:04 | |||
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Basic electron microscopy of aquatic viruses Resource Report Resource Website |
Hans-W. Ackermann and Mikal Heldal | DOI:10.17504/protocols.io.drc52v | VERVE Net | This protocol is from:Hans-W. Ackermann and Mikal Heldal. 2010. Chapter 18: Basic electron microscopy of aquatic viruses. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the full manuscript for additional details. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_182.pdf | 1 | 2015 | Hans-W. Ackermann and Mikal Heldal 2015. Basic electron microscopy of aquatic viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.drc52v | 2021-04-15 09:17:06 |
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