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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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PSS2 PCR Protocol Resource Report Resource Website |
Mel Duhaime | DOI:10.17504/protocols.io.dfm3k5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Mel Duhaime 2016. PSS2 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfm3k5 | 2021-04-15 09:14:22 | ||||
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Construction of microarrays and their application to virus analysis Resource Report Resource Website |
Michael J. Allen, Bela Tiwari, Matthias E. Futschik, and Debbie Lindell | DOI:10.17504/protocols.io.d3e8jd | VERVE Net | 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. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_034.pdf | 1 | 2015 | 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 | 2021-04-15 09:14:22 | ||
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Extinction dilution cloning for isolation of viruses infecting protists Resource Report Resource Website |
Keizo Nagasaki and Gunnar Bratbak | DOI:10.17504/protocols.io.dpx5pm | VERVE Net | 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. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_092.pdf | 1 | 2015 | 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 | 2021-04-15 09:14:21 | ||
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Characterization of the diversity of marine RNA viruses Resource Report Resource Website |
Alexander I. Culley, Curtis A. Suttle, and Grieg F. Steward | DOI:10.17504/protocols.io.dxr7m5 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | 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. | , , | 1 | 2015 | 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 | 2021-04-15 09:14:30 | |||
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Script R14: CARD Antibiotic Resistance Analysis Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejnbcme | VERVE Net, Club Grice | 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. | 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 R14: CARD Antibiotic Resistance Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejnbcme | 2021-04-15 09:14:25 | |
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VIROME Tutorials Resource Report Resource Website |
Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack | DOI:10.17504/protocols.io.d8a9sd | VERVE Net, Hurwitz Lab | 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] | , , | 1 | 2016 | Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. VIROME Tutorials. protocols.io https://dx.doi.org/10.17504/protocols.io.d8a9sd | 2021-04-15 09:14:29 | |||
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Immunoblot Screening of Chlorella Virus Plaques Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.euebete | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Immunoblot Screening of Chlorella Virus Plaques. protocols.io https://dx.doi.org/10.17504/protocols.io.euebete | 2021-04-15 09:14:25 | ||||
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Tris-glycine buffer Resource Report Resource Website |
Stanton Burnton | DOI:10.17504/protocols.io.equbdww | VERVE Net | Tris-glycine buffer solution | 1 | 2016 | Stanton Burnton 2016. Tris-glycine buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.equbdww | 2021-04-15 09:14:26 | ||||
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Script P5: Diversity Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.efrbbm6 | VERVE Net, Club Grice | 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. | 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 P5: Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.efrbbm6 | 2021-04-15 09:14:29 | |
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Manual setting of k-mer coverage peaks Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | DOI:10.17504/protocols.io.d7k9kv | VERVE Net, Hurwitz Lab | 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. | Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab | http://metavelvet.dna.bio.keio.ac.jp/MV.html | 1 | 2016 | 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 | 2021-04-15 09:14:25 | ||
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EDTA disodium salt dihydrate Resource Report Resource Website |
James Thornton | DOI:10.17504/protocols.io.dbm2k5 | VERVE Net, Sullivan Lab | For use in DNase I Treatment protocol for DNase inactivation. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 | 2021-04-15 09:14:34 | |||
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Protocol for Bacterial Heterotrophic Production Resource Report Resource Website |
Jed Fuhrman | DOI:10.17504/protocols.io.dmd425 | VERVE Net, Fuhrman Lab | Fuhrman Lab | 1 | 2015 | Jed Fuhrman 2015. Protocol for Bacterial Heterotrophic Production. protocols.io https://dx.doi.org/10.17504/protocols.io.dmd425 | 2021-04-15 09:14:33 | ||||
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1X CviJI Assay Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.espbedn | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. 1X CviJI Assay Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.espbedn | 2021-04-15 09:14:28 | ||||
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Coring Technique Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c3zyp5 | VERVE Net, Sullivan Lab | 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. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. Coring Technique. protocols.io https://dx.doi.org/10.17504/protocols.io.c3zyp5 | 2021-04-15 09:14:31 | |||
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One-step growth curves for Cellulophaga phages Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddh235 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddh235 | 2021-04-15 09:14:27 | ||||
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Zobell Agar/Broth Medium Resource Report Resource Website |
Shalaja Srinagesh et al | DOI:10.17504/protocols.io.dbn2md | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbn2md | 2021-04-15 09:14:33 | ||||
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Script P7: Assigning Whole Metagenome Taxonomy Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.egubbww | VERVE Net, Club Grice | 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. | 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 P7: Assigning Whole Metagenome Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.egubbww | 2021-04-15 09:14:26 | |
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Double SPRI for Second Generation Sequencing Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c53y8m | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c53y8m | 2021-04-15 09:14:30 | ||||
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DNA Preparation and Linker Amplification for Pyrosequencing Resource Report Resource Website |
Bonnie Poulos, Melissa Duhaime, Li Deng | DOI:10.17504/protocols.io.c9zz75 | VERVE Net, Sullivan Lab | 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. | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | 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 | 2021-04-15 09:14:28 | |||
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Roseobacter Screening Of Surface Waters For Viruses Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dbt2nm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Roseobacter Screening Of Surface Waters For Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dbt2nm | 2021-04-15 09:14:40 |
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