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Authors: Mel Duhaime
Group: VERVE Net, Sullivan Lab

Proper citation: Mel Duhaime 2016. PSS2 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfm3k5 Copy   

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Authors: Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell
Group: VERVE Net
Summary: In this virus-focused chapter, we deal primarily with the use of microarrays for expression analysis (the most popular usage) of host and virus systems during infection. We examine aspects related to array platform choice (spotted and oligonucleotide arrays), probe and array design considerations, experimental procedures and data analysis, normalization, processing, and curation. We also provide in-depth examples for the study of viral transcriptome analysis for both spotted long oligonucleotide (coccolithoviruses) and Affymetrix GeneChip (cyanophage) arrays.

Proper citation: Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell 2015. Construction of microarrays and their application to virus analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.d3e8jd Copy   

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Authors: Keizo Nagasaki and Gunnar Bratbak
Group: VERVE Net
Summary: This is a detailed outline of the extinction dilution method from: Nagasaki, K., and G. Bratbak. 2010. Isolation of viruses infecting photosynthetic and nonphotosynthetic protists, p. 92–101. 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: Keizo Nagasaki and Gunnar Bratbak 2015. Extinction dilution cloning for isolation of viruses infecting protists. protocols.io https://dx.doi.org/10.17504/protocols.io.dpx5pm Copy   

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Authors: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known about the composition, dynamics, and ecology of the RNA virioplankton. In this collection, we describe two methods to assess RNA virus diversity from seawater.

Proper citation: Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward 2015. Characterization of the diversity of marine RNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dxr7m5 Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines our analysis of the potential antibiotic resistance genes found within the skin virome. We start by visualizing the relative abundances of the top 10 antibiotic resistance categories (according to the CARD). We then quantify the number of unique antibiotic resistance gene categories annotated in the samples at each skin site, and also look at the percent CARD annotated ORFs of the overall ORFs present in each sample at each skin site.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R14: CARD Antibiotic Resistance Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejnbcme Copy   

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Authors: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: A collection of tutorials for the VIROME application. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] 

Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME Tutorials. protocols.io https://dx.doi.org/10.17504/protocols.io.d8a9sd Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Immunoblot Screening of Chlorella Virus Plaques. protocols.io https://dx.doi.org/10.17504/protocols.io.euebete Copy   

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Authors: Stanton Burnton
Group: VERVE Net
Summary: Tris-glycine buffer solution

Proper citation: Stanton Burnton 2016. Tris-glycine buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.equbdww Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method to predict phage community diversity using the algorithm PHACCS. Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the algorithm PHACCS (PHAge Communities from Contig Spectra) was developed to predict virus community alpha diversity without the use of taxonomic references. 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 P5: Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.efrbbm6 Copy   

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Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Contrary to single-genome assemblers (e.g., Velvet and SOAPdenovo), MetaVelvet assumes metagenomics settings. Accordingly, k-mer coverage histogram might be multi-modal rather than uni-modal. Please note that the coverage peak parameters can largely affect MetaVelvet assembling results. Although simple and automatic peak detection algorithm is implemented in meta-velvetg, we strongly recommend manual inspection of k-mer coverage peaks and manual setting of the coverage peak parameters. For manually setting the coverage peak parameters, please execute the following procedures.

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Manual setting of k-mer coverage peaks. protocols.io https://dx.doi.org/10.17504/protocols.io.d7k9kv Copy   

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Authors: James Thornton
Group: VERVE Net, Sullivan Lab
Summary: For use in DNase I Treatment protocol for DNase inactivation.

Proper citation: James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 Copy   

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Authors: Jed Fuhrman
Group: VERVE Net, Fuhrman Lab

Proper citation: Jed Fuhrman 2015. Protocol for Bacterial Heterotrophic Production. protocols.io https://dx.doi.org/10.17504/protocols.io.dmd425 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. 1X CviJI Assay Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.espbedn Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: This is a technique for isolating phage from agar plates. When working with lytic phage, well-isolated, cleared areas in a lawn of bacteria (called plaques) are removed from the agar (by coring with a sterile pipette) and used to infect fresh bacteria in liquid medium. The lysed culture can be used for a new plaque assay after 0.2 um filtering to remove residual bacteria. New phage are "plaque-purified" a minimum of three times before they are considered to be free of other phage.

Proper citation: Matthew Sullivan Lab 2015. Coring Technique. protocols.io https://dx.doi.org/10.17504/protocols.io.c3zyp5 Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddh235 Copy   

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Authors: Shalaja Srinagesh et al
Group: VERVE Net, Sullivan Lab

Proper citation: Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbn2md Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for assigning whole metagenome taxonomy using MetaPhlAn and MEGAN toolkits. 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 P7: Assigning Whole Metagenome Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.egubbww Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c53y8m Copy   

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Authors: Bonnie Poulos, Melissa Duhaime, Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Here, we adapt the linker amplified shotgun library (LASL) approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a “reconditioning PCR” step to increase yield and minimize late-cycle PCR artifacts. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent.Adapted from the Broad’s LASL Sanger Seq’g Protocol, and optimized for low template work.

Proper citation: Bonnie Poulos, Melissa Duhaime, Li Deng 2016. DNA Preparation and Linker Amplification for Pyrosequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c9zz75 Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Roseobacter Screening Of Surface Waters For Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dbt2nm Copy   

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