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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Clonal virus purification Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqp5vm | VERVE Net | For use in "Obtaining pure cyanophage stocks (liquid assay)" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Clonal virus purification. protocols.io https://dx.doi.org/10.17504/protocols.io.dqp5vm | 2021-04-15 09:14:51 | |||
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Isotopic Labeling of Cyanobacteria and DNA Analysis Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.c9nz5d | VERVE Net, Sullivan Lab | Protocol for labeling bacteria with N15. The bacterial DNA was made “heavy” so that community viral and host bacterial DNA could be distinguished from each other after sorting by using density gradient centrifugation. | Matthew Sullivan Lab | 1 | 2016 | Bonnie Poulos 2016. Isotopic Labeling of Cyanobacteria and DNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.c9nz5d | 2021-04-15 09:15:20 | |||
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FVIC (Frequency of Visibly Infected Cells) Protocol Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dbp2mm | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly infected cells (FVIC), the frequency of infected cells (FIC), the fraction of mortality due to viral lysis (FMVL), and burst size. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. FVIC (Frequency of Visibly Infected Cells) Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dbp2mm | 2021-04-15 09:15:20 | |||
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0.5M EDTA Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5wy7d | VERVE Net, Sullivan Lab | This shows how to make 0.5M EDTA | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c5wy7d | 2021-04-15 09:14:56 | |||
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The construction and analysis of marker gene libraries Resource Report Resource Website |
Steven M. Short, Feng Chen, and Steven W. Wilhelm | DOI:10.17504/protocols.io.dpi5kd | VERVE Net | Marker genes for viruses are typically amplified from aquatic samples to determine whether specific viruses are present in the sample, or to examine the diversity of a group of related viruses. In this [protocol], we will provide an overview of common methods used to amplify, clone, sequence, and analyze virus marker genes, and will focus our discussion on viruses infecting algae, bacteria, and heterotrophic flagellates.Short, S. M., F. Chen, and S. W. Wilhelm. 2010. The construction and analysis of marker gene libraries, p. 82–91. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2015 | Steven M. Short, Feng Chen, and Steven W. Wilhelm 2015. The construction and analysis of marker gene libraries. protocols.io https://dx.doi.org/10.17504/protocols.io.dpi5kd | 2021-04-15 09:15:27 | |||
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Gradient Recipes Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eufbetn | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Gradient Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.eufbetn | 2021-04-15 09:15:29 | ||||
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Lowry Protein Assay Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etxbepn | VERVE Net, Fish behavior and physiology, Medicinal Plants Southeastern Pará Research Group | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Lowry Protein Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.etxbepn | 2021-04-15 09:14:57 | ||||
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Resuspension Buffer P1 Resource Report Resource Website |
Qiagen | DOI:10.17504/protocols.io.hxgb7jw | VERVE Net, Sullivan Lab | This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A | Matthew Sullivan Lab, University of Arizona, The Ohio State University | http://people.mbi.ucla.edu/sumchan/qiagenbuffer.html | 2 | 2017 | Qiagen 2017. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.hxgb7jw | 2021-04-15 09:15:30 | ||
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Heald Lab Margaritas Resource Report Resource Website |
Rebecca Heald Lab | DOI:10.17504/protocols.io.ea8bahw | VERVE Net | This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here. | protocols.io | https://mcb.berkeley.edu/labs/heald/Protocols/Preparation%20of%20Heald%20Lab%20Margaritas.pdf | 1 | 2015 | Rebecca Heald Lab 2015. Heald Lab Margaritas. protocols.io https://dx.doi.org/10.17504/protocols.io.ea8bahw | 2021-04-15 09:15:32 | ||
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VBRC Base By Base: Export a sequence selection to a different file Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.eckbauw | VERVE Net, Upton-Lab | 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 | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Export a sequence selection to a different file. protocols.io https://dx.doi.org/10.17504/protocols.io.eckbauw | 2021-04-15 09:15:30 | ||
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Obtaining pure cyanophage stocks (plaque purification) Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqq5vv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Obtaining pure cyanophage stocks (plaque purification). protocols.io https://dx.doi.org/10.17504/protocols.io.dqq5vv | 2021-04-15 09:15:35 | |||
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Exotic Lab Methods Resource Report Resource Website |
Numerous scientists | DOI:10.17504/protocols.io.ebhbaj6 | VERVE Net | This collection is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.If you know creative/unusual protocols like these, please tweet them to #ExoticMethods, e-mail to "[email protected]", or share directly as a protocol here, tagging with "ExoticMethods". | University of Arizona | 1 | 2016 | Numerous scientists 2016. Exotic Lab Methods. protocols.io https://dx.doi.org/10.17504/protocols.io.ebhbaj6 | 2021-04-15 09:15:05 | |||
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16S PCR Universal Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.c5my45 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Natalie Solonenko 2016. 16S PCR Universal. protocols.io https://dx.doi.org/10.17504/protocols.io.c5my45 | 2021-04-15 09:15:35 | ||||
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VBRC Base By Base: View gene annotations Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecqbavw | VERVE Net, Upton-Lab | 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 | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: View gene annotations. protocols.io https://dx.doi.org/10.17504/protocols.io.ecqbavw | 2021-04-15 09:15:06 | ||
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One-Step Growth Curves for Cyanophages Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dan2dd | VERVE Net, Sullivan Lab | Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. One-Step Growth Curves for Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.dan2dd | 2021-04-15 09:15:36 | ||||
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Isolation and Purification of Plasmid DNA from E. coli Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ertbd6n | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Isolation and Purification of Plasmid DNA from E. coli. protocols.io https://dx.doi.org/10.17504/protocols.io.ertbd6n | 2021-04-15 09:15:09 | ||||
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MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | DOI:10.17504/protocols.io.d7q9mv | VERVE Net, Hurwitz Lab | Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome. | Hurwitz Lab, Hurwitz Lab, Hurwitz Lab, Hurwitz Lab, Hurwitz Lab, Hurwitz Lab | 1 | 2016 | Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. protocols.io https://dx.doi.org/10.17504/protocols.io.d7q9mv | 2021-04-15 09:15:36 | |||
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Running "16sblaster" at iPlant Resource Report Resource Website |
Ken Youens-Clark | DOI:10.17504/protocols.io.egmbbu6 | VERVE Net, Hurwitz Lab | See upcoming paper by Watts, Hurwitz, Youens-Clark.Code is freely available at Github. | University of Arizona | 1 | 2016 | Ken Youens-Clark 2016. Running "16sblaster" at iPlant. protocols.io https://dx.doi.org/10.17504/protocols.io.egmbbu6 | 2021-04-15 09:15:36 | |||
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Script R7: Intra and Inter Personal Dissimilarity Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.eipbcdn | VERVE Net, Club Grice | This protocol outlines the analysis used for intra and interpersonal diversity of the virome and whole metagenome using the Bray Curtis dissimilarity metric. We visualize the differences as bar plots and calculate the statistical significance of the differences using a t-test. 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. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R7: Intra and Inter Personal Dissimilarity. protocols.io https://dx.doi.org/10.17504/protocols.io.eipbcdn | 2021-04-15 09:15:09 | |
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Preparation of PBCV-1 Lysin Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etdbei6 | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Preparation of PBCV-1 Lysin. protocols.io https://dx.doi.org/10.17504/protocols.io.etdbei6 | 2021-04-15 09:15:11 |
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