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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Resuspension Buffer P1 Resource Report Resource Website |
Qiagen | DOI:10.17504/protocols.io.c49yz5 | 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 | 1 | 2015 | Qiagen 2015. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.c49yz5 | 2021-04-15 09:16:09 | ||
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VBRC Base By Base: Import genome sequences from Virology.ca viral databases Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecjbaun | 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: Import genome sequences from Virology.ca viral databases. protocols.io https://dx.doi.org/10.17504/protocols.io.ecjbaun | 2021-04-15 09:16:09 | ||
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Lysate titer Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqn5vd | 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. Lysate titer. protocols.io https://dx.doi.org/10.17504/protocols.io.dqn5vd | 2021-04-15 09:16:11 | |||
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g23 T4-type (myovirus) PCR Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfq3mv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. g23 T4-type (myovirus) PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfq3mv | 2021-04-15 09:16:17 | ||||
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RNAlater Recipe Resource Report Resource Website |
Rex Malmstrom | DOI:10.17504/protocols.io.c56y9d | VERVE Net, Sullivan Lab | This is a storage solution that stabilizes and protectsRNA while inactivating RNase | MIT/Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Rex Malmstrom 2015. RNAlater Recipe. protocols.io https://dx.doi.org/10.17504/protocols.io.c56y9d | 2021-04-15 09:16:18 | |||
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Mapping Metagenomic Reads to Reference Sequences (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.gv2bw8e | VERVE Net, Sullivan Lab, iVirus | Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter. | The Ohio State University | 3 | 2016 | Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gv2bw8e | 2021-04-15 09:16:17 | |||
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Purification of viruses from culture lysates Resource Report Resource Website |
Janice E. Lawrence and Grieg F. Steward | DOI:10.17504/protocols.io.d2t8em | VERVE Net | Ultracentrifugation provides a means to concentrate, analyze, and purify viruses in solution, and therefore represents an invaluable tool for aquatic virologists. This protocol provides a method for purification of viruses from culture lysates from natural water samples. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_166.pdf | 1 | 2015 | Janice E. Lawrence and Grieg F. Steward 2015. Purification of viruses from culture lysates. protocols.io https://dx.doi.org/10.17504/protocols.io.d2t8em | 2021-04-15 09:16:24 | ||
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Detecting Fungal Infections in Almonds Resource Report Resource Website |
Carolina Cadena | DOI:10.17504/protocols.io.etnbeme | VERVE Net | This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format. Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72 | 1 | 2016 | Carolina Cadena 2016. Detecting Fungal Infections in Almonds. protocols.io https://dx.doi.org/10.17504/protocols.io.etnbeme | 2021-04-15 09:16:14 | ||||
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Dot Blot Preparation Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etibeke | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Dot Blot Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.etibeke | 2021-04-15 09:16:14 | ||||
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MECH step CsCl density gradients Resource Report Resource Website |
KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN | DOI:10.17504/protocols.io.ek5bcy6 | VERVE Net | For use in Generating viral metagenomes from the coral holobiont. | , , , | 1 | 2016 | KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN 2016. MECH step CsCl density gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.ek5bcy6 | 2021-04-15 09:16:17 | |||
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0.5M NH4Cl Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c77zrm | VERVE Net, Sullivan Lab | Supplement to seawater for growth of cyanobacteria. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io https://dx.doi.org/10.17504/protocols.io.c77zrm | 2021-04-15 09:16:16 | |||
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Phenol-chloroform extraction with ethanol precipitation Resource Report Resource Website |
Grieg F. Steward and Alexander I. Culley | DOI:10.17504/protocols.io.dsb6am | VERVE Net | The traditional phenol extraction procedure, based on early work by Kirby (1957) and elaborated in most modern protocol compendia, yields very clean nucleic acids suitable for a variety of downstream applications. This extraction method is coupled with a routine alcohol precipitation step to allow buffer exchange, removal of trace amounts of chloroform, and concentration of nucleic acids (Sambrook and Russell 2001).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. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_154.pdf | 1 | 2015 | Grieg F. Steward and Alexander I. Culley 2015. Phenol-chloroform extraction with ethanol precipitation. protocols.io https://dx.doi.org/10.17504/protocols.io.dsb6am | 2021-04-15 09:16:30 | ||
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Isolation of cyanophages by liquid bioassays Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dp25qd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Multiwell plates are convenient for isolating cyanophages from environmental samples using the liquid bioassay approach (Table 1). This protocol describes a typical procedure (96-well assay) used to detect and isolate cyanophages from marine samples that lyses Synechococcus sp. strain DC2 (also known as CCMP1334 or WH7803). Using this method, greater than 105 lytic phages per milliliter of seawater have been detected in the Gulf of Mexico (Suttle and Chan 1994) that lyses this permissive target host. | 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. Isolation of cyanophages by liquid bioassays. protocols.io https://dx.doi.org/10.17504/protocols.io.dp25qd | 2021-04-15 09:16:20 | ||
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PBCV-1 Virus Plaque Assay Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.estbeen | VERVE Net | PBCV-1 is a large plaque virus (approximately 2-3 mm in diameter). The plaque size of the viruses reflects the length of the virus replication cycle. PBCV-1 has a life cycle of about 6-8 hours. When titering you should use plates that were poured no more than 1 day before the time of use. Variable plaque formation will result if fresh plates are not used. (This is similar to a phage phenomenon.) Pyrex petri dishes do give more uniform plaque formation versus the plastic, however this is not so critical as with slower growing NC64A viruses. | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. PBCV-1 Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.estbeen | 2021-04-15 09:16:33 | |||
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VBRC Base By Base: Switching between Mouse Modes Resource Report Resource Website |
Nick Tang | DOI:10.17504/protocols.io.ecpbavn | 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: Switching between Mouse Modes. protocols.io https://dx.doi.org/10.17504/protocols.io.ecpbavn | 2021-04-15 09:16:31 | ||
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SPOT DNA Extraction from 142mm Durapore 0.22µm Filters Resource Report Resource Website |
Rohan Sachdeva, Cheryl Chow | DOI:10.17504/protocols.io.dmi44d | VERVE Net, Fuhrman Lab | Reference: Fuhrman et al, 1988. Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies. AEM 54(6), 1426‐1429 | Fuhrman Lab, Fuhrman Lab | 1 | 2015 | Rohan Sachdeva, Cheryl Chow 2015. SPOT DNA Extraction from 142mm Durapore 0.22µm Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.dmi44d | 2021-04-15 09:16:23 | |||
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Formulation of FES Medium Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eucbesw | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Formulation of FES Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.eucbesw | 2021-04-15 09:16:38 | ||||
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Electron Microscopy of Haloviruses Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.ebbbain | VERVE Net | 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. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_057.pdf | 1 | 2016 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Electron Microscopy of Haloviruses. protocols.io https://dx.doi.org/10.17504/protocols.io.ebbbain | 2021-04-15 09:16:40 | ||
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Preparation of Tara Sample DNA From Iron-Chloride Precipitates Resource Report Resource Website |
Matt Sullivan Lab | DOI:10.17504/protocols.io.c24ygv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Matt Sullivan Lab 2016. Preparation of Tara Sample DNA From Iron-Chloride Precipitates. protocols.io https://dx.doi.org/10.17504/protocols.io.c24ygv | 2021-04-15 09:16:22 | ||||
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Script P6: HPyV Detection Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.efxbbpn | VERVE Net, Club Grice | This protocol provides a method for detecting Human Polyomaviruses (HPyVs) in our virome and whole metagenome datasets. For genome reference, download the HPyV genomes (in fasta format) from NCBI (nucleotide) using the search terms "Human Polyomavirus" AND "Complete Genome". This is used in the rest of the analyses. 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 | Grice Lab, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, Grice Lab, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, Grice Lab, 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 P6: HPyV Detection. protocols.io https://dx.doi.org/10.17504/protocols.io.efxbbpn | 2021-04-15 09:16:39 |
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