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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The following are media recipes necessary for isolating and maintaining Synechococcus isolates.

Proper citation: Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io https://dx.doi.org/10.17504/protocols.io.c9jz4m Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Colony PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6czav Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Summary: Recipe to make 10ml of 2x stock

Proper citation: David Dunigan and Irina Agarkova 2016. SDS-PAGE Cracking Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.erpbd5n Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. CviJI Purification From IL-3A Virus Infected NC64A Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.er3bd8n Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Buffer B, pH 8.5. protocols.io https://dx.doi.org/10.17504/protocols.io.eskbecw 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. Running gel buffer (10X). protocols.io https://dx.doi.org/10.17504/protocols.io.ercbd2w Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. YTSS Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbq2mv Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Restriction Endonuclease Purification From Virus Infected Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.errbd56 Copy   

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Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: These are protocols 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. The Isolation of Viruses Infecting Archaea. protocols.io https://dx.doi.org/10.17504/protocols.io.ebibake Copy   

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Authors: Grieg F. Steward and Alexander I. Culley
Group: VERVE Net
Summary: If one has a purified stock of viruses obtained, for example, by banding in a buoyant density gradient, or even a relatively pure viral concentrate obtained by size fractionation, it is possible to release the DNA in a high molecular weight form suitable for some applications (e.g., pulsed-field gel electrophoresis [PFGE] for sizing or probing, or nucleic acid quantification by fluorescence) relatively simply. This method involves exchanging the buffer in which the viruses are suspended with one containing EDTA and SDS, followed by heating. The method is similar to that described previously (Steward 2001), but with the optional addition of detergent to facilitate disintegration of the viral capsid.This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses. 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: Grieg F. Steward and Alexander I. Culley 2015. Release of nucleic acids with heat, chelator, and detergent. protocols.io https://dx.doi.org/10.17504/protocols.io.dsc6av Copy   

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Authors: Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA
Group: VERVE Net, Club Grice
Summary: This collection contains protocols for the computational analysis performed in the paper "The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome". Geoffrey Hannigan and Jacquelyn Meisel are graduate students in Dr. Elizabeth Grice's lab in the Department of Dermatology at the University of Pennsylvania.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, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA 2016. The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.ekubcww Copy   

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Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: In this protocol we show how to perform the taxonomic biomarker discovery operation using LEfSe.

Proper citation: Curtis Huttenhower 2016. Taxonomic biomarker discovery with LEfSe. protocols.io https://dx.doi.org/10.17504/protocols.io.d9699d Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocols outlines our definitions of core operational protein families (OPFs), potential auxiliary metabolic genes (AMGs), sharing of genes across anatomical sites, and Bray-Curtis dissimilarity of the OPFs by anatomical site. 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 R13: OPF and AMG Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejkbckw Copy   

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Authors: Li Deng
Group: VERVE Net, Sullivan Lab

Proper citation: Li Deng 2016. SYBR Gold working solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.c7azid Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative abundance approach by visualizing the percent of temperate phages present at each site. We end by visualizing the relative abundances of bacteria annotations of the phage contigs. 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 R11: Replication Cycle. protocols.io https://dx.doi.org/10.17504/protocols.io.ejfbcjn 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: Import genes from Genbank file. protocols.io https://dx.doi.org/10.17504/protocols.io.ecxbaxn Copy   

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Authors: William H. Wilson and Declan Schroeder
Group: VERVE Net

Proper citation: William H. Wilson and Declan Schroeder 2016. Generation of DNA fragments by sonication. protocols.io https://dx.doi.org/10.17504/protocols.io.dy57y5 Copy   

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Authors: Janice E. Lawrence and Grieg F. Steward
Group: VERVE Net
Summary: Lawrence, J. E., and G. F. Steward. 2010. Purification of viruses by centrifugation, p. 166–181. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the published manuscript for additional information.

Proper citation: Janice E. Lawrence and Grieg F. Steward 2015. Purification of viruses by centrifugation. protocols.io https://dx.doi.org/10.17504/protocols.io.d2v8e5 Copy   

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Authors: Dr. Steven Wilhelm, Samantha Coy
Group: VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Ultracentrifugation in the WX Ultra Series can support only 30 mL samples at a time, and therefore do not significantly concentrate viruses. Tangential flow filtration enables viral concentration of large volumes that can then be purified using sucrose density gradients. Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.hgrb3v6 Copy   

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Authors: Curtis Huttenhower
Group: VERVE Net, Huttenhower Lab
Summary: This tutorial focuses on performing a comprehensive metagenomic analysis from whole-genome shotgun sequencing data for microbiome studies. It is divided in to different steps that use the following metagenomic, computational tools: MetaPhlAn, GraPhlAn, LEfSe, and HUMAnN. Our last addition to the PhlAn tools is PhyloPhlAn that can be used in metagenomics for phylgenetically and taxonomically place contigs assembled from whole metagenomic sequencing samples.This tutorial is also a step-by-step description of the metagenomic pipeline we used in our review paper about computational meta'omics (specifically Figure 4).

Proper citation: Curtis Huttenhower 2016. bioBakery Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.d9899v Copy   

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