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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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1M Tris Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5vy65 | VERVE Net, Sullivan Lab | This shows how to make 1M Tris. | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. 1M Tris. protocols.io https://dx.doi.org/10.17504/protocols.io.c5vy65 | 2021-04-15 09:16:19 | |||
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g20 (myovirus) PCR Protocol Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.dam2c5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Li Deng 2016. g20 (myovirus) PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dam2c5 | 2021-04-15 09:16:19 | ||||
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Phenol extraction of Chlorella cells Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eshbeb6 | VERVE Net | University of Nebraska-Lincoln | http://www.lclane.net/text/chlorellaphenol.html | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Phenol extraction of Chlorella cells. protocols.io https://dx.doi.org/10.17504/protocols.io.eshbeb6 | 2021-04-15 09:16:21 | |||
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Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eq7bdzn | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride. protocols.io https://dx.doi.org/10.17504/protocols.io.eq7bdzn | 2021-04-15 09:16:40 | ||||
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Comparative metagenomic analysis using VIROME Resource Report Resource Website |
Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack | DOI:10.17504/protocols.io.d7j9km | VERVE Net, Hurwitz Lab | This tutorial demonstrates the use of VIROME for comparing viral metagenome libraries analyzed with the VIROME pipeline as well as comparative analysis of viral communities using the Quantitative Insights in Microbial Ecology package (QIIME). 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] See site for more information. | , , | http://virome.dbi.udel.edu/ | 1 | 2016 | Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. Comparative metagenomic analysis using VIROME. protocols.io https://dx.doi.org/10.17504/protocols.io.d7j9km | 2021-04-15 09:16:41 | ||
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Script R16: CRISPR Analysis Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejqbcmw | VERVE Net, Club Grice | This protocol outlines how to generate tables to analyze CRISPR interactions. Based on 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 R16: CRISPR Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejqbcmw | 2021-04-15 09:16:38 | |
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Remove unadsorbed phages Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.drb52m | VERVE Net | For use in "One-step growth experiments (cyanophages)" | 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. Remove unadsorbed phages. protocols.io https://dx.doi.org/10.17504/protocols.io.drb52m | 2021-04-15 09:16:37 | |||
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Marine Basal Media Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dcc2sv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Marine Basal Media. protocols.io https://dx.doi.org/10.17504/protocols.io.dcc2sv | 2021-04-15 09:16:37 | ||||
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Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek3bcyn | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ek3bcyn | 2021-04-15 09:16:21 | |||
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Script P3: Open Reading Frame Prediction Resource Report Resource Website |
HANNIGAN GC, GRICE EA, ET AL | DOI:10.17504/protocols.io.efpbbmn | VERVE Net, Club Grice | This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods based on the 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 GC, GRICE EA, ET AL 2016. Script P3: Open Reading Frame Prediction. protocols.io https://dx.doi.org/10.17504/protocols.io.efpbbmn | 2021-04-15 09:16:47 | |
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One-step growth experiments (cyanophages) Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dra52d | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on Synechococcus sp. BBC1 (Suttle and Chan 1993). | 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. One-step growth experiments (cyanophages). protocols.io https://dx.doi.org/10.17504/protocols.io.dra52d | 2021-04-15 09:16:47 | ||
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16S Universal Bacterial PCR Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfr3m5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dfr3m5 | 2021-04-15 09:16:25 | ||||
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PCTE filter staining Resource Report Resource Website |
Ken Stedman | DOI:10.17504/protocols.io.eavbae6 | VERVE Net | For use in "PCTE Protocol for VLP enumeration" | Stedman Lab | 1 | 2016 | Ken Stedman 2016. PCTE filter staining. protocols.io https://dx.doi.org/10.17504/protocols.io.eavbae6 | 2021-04-15 09:16:23 | |||
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Viruses from Sulfolobus and close relatives Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.dpb5im | VERVE Net | The following methods are basically method “A” of Zillig et al. (1994) and were described recently in detail by Prangishvili (2006). These methods consist of enrichment cultures followed by host isolation and screening for virus production in both these isolates and enrichment cultures. These techniques are very similar to those used for bacteriophages, with the major exception being the extreme growth conditions (80˚C, pH 3).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 | 2015 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2015. Viruses from Sulfolobus and close relatives. protocols.io https://dx.doi.org/10.17504/protocols.io.dpb5im | 2021-04-15 09:16:26 | ||
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Cesium Chloride Dialysis for Viruses Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7jzkm | VERVE Net, Sullivan Lab | Version 3This protocol describes the use of Cesium Chloride to purify viruses with an optional dialysis step to remove the CsCl. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012.References:Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 15(5), 1428–1440. doi:10.1111/j.1462-2920.2012.02836.x. | University of Arizona, Ohio State University | http://www.eebweb.arizona.edu/faculty/mbsulli/protocols/protocols/CsCl_Virus_Purification_Dialysis_v3.pdf | 1 | 2016 | Matthew Sullivan 2016. Cesium Chloride Dialysis for Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.c7jzkm | 2021-04-15 09:16:52 | ||
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Microbubbling technique Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.egkbbuw | VERVE Net, Sullivan Lab | For use in the protocol "Large Volume Marine Cyanophage protocols" | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Microbubbling technique. protocols.io https://dx.doi.org/10.17504/protocols.io.egkbbuw | 2021-04-15 09:16:27 | |||
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PCR amplification of the SISPA primer reaction mixture 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.emebc3e | 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. PCR amplification of the SISPA primer reaction mixture. protocols.io https://dx.doi.org/10.17504/protocols.io.emebc3e | 2021-04-15 09:16:27 | |||
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Adsorbing Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dar2d5 | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with high concentrations of viruses. For natural samples, use the protocol “Quantitatively Depositing Viruses onto TEM Grids using an Airfuge”.Note: If purification of the viruses is necessary, refer to Ackermann and Heldal (2010) for various options. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Adsorbing Viruses on TEM Grids. protocols.io https://dx.doi.org/10.17504/protocols.io.dar2d5 | 2021-04-15 09:16:51 | |||
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SYBR Gold Staining for Viral Enumeration (Case 2) Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7fzjm | VERVE Net, Sullivan Lab | Case 2: Fix samples. Use this protocol when long term storage of slide is required.For when you can count your samples in a few days, see Case 1. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 2). protocols.io https://dx.doi.org/10.17504/protocols.io.c7fzjm | 2021-04-15 09:16:50 | |||
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Script R5: Virome Alpha Diversity Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.eimbcc6 | VERVE Net, Club Grice | This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. 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 R5: Virome Alpha Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.eimbcc6 | 2021-04-15 09:16:53 |
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