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Authors: Curtis A. Suttle and Jed A. Fuhrman
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: For Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy protocol.
Proper citation: Curtis A. Suttle and Jed A. Fuhrman 2015. Preparation of reagents. protocols.io https://dx.doi.org/10.17504/protocols.io.dqj5um Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stock: plaque purification"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Plate Amplification. protocols.io https://dx.doi.org/10.17504/protocols.io.dq75zm Copy
Authors: Curtis A. Suttle and Jed A. Fuhrman
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: For Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy protocol.
Proper citation: Curtis A. Suttle and Jed A. Fuhrman 2015. Sample collection and preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.dqk5uv Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: 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.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R10: Whole Metagenome Beta Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.ejebcje Copy
Authors: Jonathan King Lab
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Jonathan King Lab 2016. CsCl Step Gradient to Purify Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c4zyx5 Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: 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
Proper citation: 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 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Artificial Seawater Based AMP1 Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.c9mz45 Copy
Authors: Forest Rohwer
Group: VERVE Net, Sullivan Lab
Summary: 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
Proper citation: Forest Rohwer 2016. Cesium Chloride Protocol for Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c37yrm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.deq3dv Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Bonnie Poulos 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.ekrbcv6 Copy
Authors: Corina Brussaard, Anne-Claire Baudoux, Anna A. M. Noordeloos, Marcel J. W. Veldhuis
Group: VERVE Net
Summary: An alternate version to the protocol "Simultaneous measurement of grazing and viral lysis of phytoplankton v1"
Proper citation: 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 Copy
Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: 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.
Proper citation: 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 Copy
Authors: Jed Fuhrman
Group: VERVE Net, Fuhrman Lab
Summary: For use in "SYBR Green Assay".
Proper citation: Jed Fuhrman 2015. Filter drying procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.dju4nv Copy
Authors: Jozef Nissimov
Group: VERVE Net, Bidle Lab
Summary: Purification of viruses via CsCl gradient and ultracentrifugation
Proper citation: Jozef Nissimov 2015. Purification of viruses via CsCl gradient and ultracentrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.d9k94v Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol.
Proper citation: Matthew Sullivan 2016. Non-Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddk24v Copy
Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: 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
Proper citation: Curtis Huttenhower 2016. Metabolic profiling with HUMAnN. protocols.io https://dx.doi.org/10.17504/protocols.io.d9799m Copy
Authors: Simon Roux, Francois Enault, Bonnie L. Hurwitz, Matthew B. Sullivan
Group: VERVE Net, Hurwitz Lab, Plantae
Summary: This protocol gives an introduction to running VirSorter in the iPlant Discovery Environment.
Proper citation: 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 Copy
Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Assay Conditions. protocols.io https://dx.doi.org/10.17504/protocols.io.es3begn Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Jennifer Brum 2016. Using ImageJ to Measure Viral Dimensions in Micrographs. protocols.io https://dx.doi.org/10.17504/protocols.io.ddf23m Copy
Authors: Hans-W. Ackermann and Mikal Heldal
Group: VERVE Net
Summary: 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.
Proper citation: Hans-W. Ackermann and Mikal Heldal 2015. Basic electron microscopy of aquatic viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.drc52v Copy
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