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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Modified after Glöckner et al. 1999

Proper citation: Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.c3ayid Copy   

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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: Align entire sequences or subsequence regions. protocols.io https://dx.doi.org/10.17504/protocols.io.ecybaxw Copy   

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Authors: Amy Zimmerman
Group: VERVE Net, Worden Lab
Summary: Purpose: To reproducibly generate fresh preparations of virus for independent experiments.Fresh virus sample for an experiment is generated by a primary infection of exponentially growing host cells from a master stock of virus. The infected host is allowed to lyse until the culture is cleared. The lysate is filtered to remove any large cellular debris, then the viral-size fraction is concentrated from the filtered lysate and washed with buffer using a centrifugal concentrator.  The viral concentrate is stored at 4°C protected from light and should be used for an experiment within 1-2 days. On the day of (or the day before) the experiment, an MPN assay should be set up to assess infectivity of the fresh viral concentrate.

Proper citation: Amy Zimmerman 2016. Propagation of marine eukaryotic viruses (Prasinoviruses). protocols.io https://dx.doi.org/10.17504/protocols.io.fcabise Copy   

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Authors: Amy Zimmerman
Group: VERVE Net, Worden Lab
Summary: Purpose: To evaluate the influence of nutrient availability on cellular elemental composition (quotas and stoichiometry) in marine picoeukaryotes.Elemental quotas and ratios are assessed under nutrient replete and deplete conditions at the same time to minimize potential variation between experiments. Cells from an exponentially growing culture are concentrated by centrifugation, washed and re-suspended in a small volume of nutrient deplete media. These concentrated cells are used to inoculate triplicate replete and deplete culture flasks at a starting density corresponding to early-exponential growth. Culture growth is monitored daily. When the mean growth rate of the nutrient deplete treatment is half or less of the replete treatment (GRDEP/GRREP

Proper citation: Amy Zimmerman 2016. Nutrient deplete/replete algal culture for elemental analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.fcdbis6 Copy   

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Authors: Hannigan GC, Grice EA, et al.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for assembly of metagenomic data using the Ray assembly toolkit and the subsequent analysis of contig statistics. Based on the 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 GC, Grice EA, et al. 2016. Script P2: Contig Assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.ed9ba96 Copy   

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Authors: Forest Rohwar
Group: VERVE Net, Sullivan Lab
Summary: In tangential flow filtration (TFF), the sample is run parallel to the filter. Particles that are smaller than the pore size are pushed out through the holes (the filtrate). Particles that are larger than the pore size are retained inside the filter (the retentate). TFF is most effective when a reservoir is used so that the sample can be recycled through numerous times.

Proper citation: Forest Rohwar 2016. Phage Tangential Flow Filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.c7yzpv Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. Cracking buffer, 4X (10 mL). protocols.io https://dx.doi.org/10.17504/protocols.io.erdbd26 Copy   

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Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab

Proper citation: Natalie Solonenko 2016. Plaque Assay Protocol for Pseudoalteromonas. protocols.io https://dx.doi.org/10.17504/protocols.io.de33gm Copy   

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Authors: Marine Phage Lab, Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.

Proper citation: Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io https://dx.doi.org/10.17504/protocols.io.c26yhd Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Extraction of DNA from Virus. protocols.io https://dx.doi.org/10.17504/protocols.io.et4beqw Copy   

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Authors: Barbra Ferrell
Group: VERVE Net, Wommack/Polson Viral Ecology and Informatics Resources (VEIL) Lab
Summary: Viral Informatics Resource for Metagenome Exploration (VIROME) is a bioinformatics pipeline that classifies viral metagenome sequences after searching against annotated reference sequence databases (i.e., UniRef, SEED, ACLAME, COG, GO, KEGG, and PhageSEED) and a custom environmental database, Metagenomes Online (MgOl). VIROME’s compare tool allows users to compare any number of metagenomes to one another by generating a Biological Observation Matrix (biom) file that contain counts of occurrences of custom observations (comparison metrics), and a mapping text file that provides per-sample metadata (library IDs and descriptions). Quantitative Insights Into Microbial Ecology (QIIME) is an open-source software pipeline that allows users to interpret raw sequencing data and create graphical displays to interact with the data. QIIME is modular, providing users with the flexibility to select and integrate various applications. While QIIME has many capabilities and online tutorials, this SOP is limited to the steps a user will take to use VIROME’s compare tool output (biom and mapping files) to explore composition (what is in a sample), alpha-diversity (diversity within a sample), and beta-diversity (comparison of diversity between samples). This SOP generally follows guidance in online tutorials but with modifications unique to the VIROME Comparinator output analysis.

Proper citation: Barbra Ferrell 2016. QIIME: VIROME comparinator tool diversity metrics. protocols.io https://dx.doi.org/10.17504/protocols.io.ec9baz6 Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the Bray-Curtis dissimilarity NMDS ordination and significance analysis of our manuscript. Here we will look at the clustering of the virome samples using our reference independent OTU table based on contig hits. We will compare skin environments (sebaceous, etc), occlusion status, and time. We also look at the difference between the background controls and the rest of the samples. 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.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R6: Virome Beta Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.einbcde Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.de23gd Copy   

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Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab

Proper citation: Bonnie Poulos 2016. Plaque Assay Protocol for Pseudoalteromonas. protocols.io https://dx.doi.org/10.17504/protocols.io.ek7bczn Copy   

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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 Buffer A. protocols.io https://dx.doi.org/10.17504/protocols.io.eswbefe Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. RNA Isolation from Viral-infected Chlorella NC64A. protocols.io https://dx.doi.org/10.17504/protocols.io.erqbd5w Copy   

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Authors: Virginia Rich
Group: VERVE Net, Sullivan Lab
Summary: Modified after V. Rich, 2/10/07: DNA extraction protocol from 25 mm 0.2 μm filters – Low-throughput, using DNeasy columns (based on lab Steripak filter extraction protocol and the Suzuki et al. 2001 protocol)

Proper citation: Virginia Rich 2016. DNA Extraction from sorted cells. protocols.io https://dx.doi.org/10.17504/protocols.io.c38yrv Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of the trace metal mixture for addition to seawater for the cultivation of marine cyanobacteria, Prochlorococcus and Synechococcus

Proper citation: Matthew Sullivan Lab 2015. Cyanobacteria Trace Metal Mixture (CTMM). protocols.io https://dx.doi.org/10.17504/protocols.io.c8nzvd Copy   

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Authors: DeLong Lab
Group: VERVE Net, Sullivan Lab
Summary: Adapted from Steripak protocol, with addition of RNase.

Proper citation: DeLong Lab 2015. Lysis Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c4ryv5 Copy   

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Authors: Stanton Burnton, Tiong Gim Aw, Samantha Wengert, Joan B. Rose
Group: VERVE Net
Summary: This protocol is a parody of an existing scientific journal article and is intended to showcase the features available on the protocols.io platform in order for VERVE Net members to develope future protocols. While the viral metagenomic analysis on Cabbage Patch Kids is impossible to perform, due to the real-world non-existant nature of Cabbage Patch kids, the sourced article is Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses written by Tiong Gim Aw, Samantha Wengert, and Joan B. Rose (included in the authors section)and the "Material and methods" section has been adapted from using actual lettuce data to a metagenomic protocol for Cabbage Patch Kids.

Proper citation: Stanton Burnton, Tiong Gim Aw, Samantha Wengert, Joan B. Rose 2016. Viral metagenomic analysis on Cabbage Patch Kids. protocols.io https://dx.doi.org/10.17504/protocols.io.es5beg6 Copy   

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