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Authors: Mathieu LAZARE
Group: VERVE Net, Martínez Martinez Lab
Summary: The purpose of this protocol is to isolate and characterize viruses that infect P.olseni, P.marinus.
Proper citation: Mathieu LAZARE 2016. Viruses Purification of Perkinsus spp.. protocols.io https://dx.doi.org/10.17504/protocols.io.er9bd96 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 of Haloviruses from Natural Waters. protocols.io https://dx.doi.org/10.17504/protocols.io.ebcbaiw Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io https://dx.doi.org/10.17504/protocols.io.dem3c5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Cellulophaga 38:1 Lytic Gene PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dfz3p5 Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. DTT solution. protocols.io https://dx.doi.org/10.17504/protocols.io.erabd2e Copy
Authors: Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman
Group: VERVE Net, Fuhrman Lab
Summary: The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from:Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc. 2007;2(2):269-76.Please see the full manuscript for more details.
Proper citation: Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman 2015. SYBR Green Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.djg4jv Copy
Authors: Seth John, Bonnie Poulos, Christine Schirmer
Group: VERVE Net, Sullivan Lab
Summary: Preparation of iron chloride resuspension buffer using disodium EDTA dihydrate and magnesium chloride in Tris buffer.
Proper citation: Seth John, Bonnie Poulos, Christine Schirmer 2015. 0.1M EDTA-0.2M MgCl2-0.2M Ascorbate Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c2yyfv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: .
Proper citation: Matthew Sullivan 2016. NaCl Sodium Chloride Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c64zgv Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ek4bcyw Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the quality control analysis measuring the percent relative abundance of 16S rRNA levels in the virome and whole metagenome, as well as the number of virome sequences mapping to the whole metagenome, and vice versa. These measures are used to validate the quality of the sequence datasets. 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 R3: Quality Control Statistics. protocols.io https://dx.doi.org/10.17504/protocols.io.eh9bb96 Copy
Authors: Curtis A. Suttle and Jed A. Fuhrman
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: This is a protocol from: Suttle, C. A. and J. A. Fuhrman. 2010. Chapter 15: Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy. 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: Curtis A. Suttle and Jed A. Fuhrman 2015. Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.dpy5pv Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Supplement to seawater for growth of cyanobacteria.
Proper citation: Matthew Sullivan Lab 2015. 0.025M NaH2PO4·H2O. protocols.io https://dx.doi.org/10.17504/protocols.io.c8czsv Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. SOB medium. protocols.io https://dx.doi.org/10.17504/protocols.io.eq8bdzw Copy
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 A. protocols.io https://dx.doi.org/10.17504/protocols.io.esibece Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Titration of AmPure XP Beads for Removal of Fragments . protocols.io https://dx.doi.org/10.17504/protocols.io.c52y8d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io https://dx.doi.org/10.17504/protocols.io.dpa5id 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: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search). protocols.io https://dx.doi.org/10.17504/protocols.io.eczbax6 Copy
Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: For use in "Isolation of cyanophages by plaque assyays"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Top agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.dqh5t5 Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses
Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. SYBR Gold Working Stock. protocols.io https://dx.doi.org/10.17504/protocols.io.c82zyd Copy
Authors: Amy Zimmerman
Group: VERVE Net, Worden Lab
Summary: Purpose: To quantify virus-like particles in culture or environmental samples.Host cells and virus-like particles are enumerated from the same glutaraldehyde-fixed sample. For virus counts, an aliquot is diluted in 0.02-µm-filtered TE buffer prior to staining with SYBR Green I nucleic acid dye to improve staining efficiency and ensure an appropriately low event rate in the instrument. An unstained aliquot of sample is run for host cell counts.
Proper citation: Amy Zimmerman 2016. Enumerating algal viruses by flow cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.fccbisw Copy
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