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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Purification of Cafeteria roenbergensis virus particles Resource Report Resource Website |
Matthias Fischer | DOI:10.17504/protocols.io.qz2dx8e | VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G) | The concentration and purification of giant DNA viruses from bacteria-containing cultures can present problems because the particle size of giant viruses overlaps with that of smaller bacteria, hence filtration as the only separation method is not possible.In this protocol, a combination of centrifugation, tangential flow filtration, and density-gradient ultracentrifugation is used to concentrate and purify particles of the giant marine virus CroV that infects the heterotrophic flagellate Cafeteria roenbergensis. | Max Planck Institute for Medical Research, Heidelberg, Germany | 1 | 2018 | Matthias Fischer 2018. Purification of Cafeteria roenbergensis virus particles. protocols.io https://dx.doi.org/10.17504/protocols.io.qz2dx8e | 2021-04-15 09:15:13 | |||
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Primary trace metal stocks Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c8hzt5 | VERVE Net, Sullivan Lab | Preparation of trace metal stock solutions for cyanobacteria trace metal mixture (CTMM) | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. Primary trace metal stocks. protocols.io https://dx.doi.org/10.17504/protocols.io.c8hzt5 | 2021-04-15 09:15:13 | |||
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Script R4: Virome Taxonomy Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.eiabcae | VERVE Net, Club Grice | This protocol outlines our bacteriophage/virus taxonomy analyses. This analysis includes profiles for the average order relative abundance for each site, the phage species relative abundance profiles for each patient, and the relative abundance of specific species between sites. Intermediate files are also included with the publication, and the paths are specified below. 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 R4: Virome Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.eiabcae | 2021-04-15 09:15:38 | |
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Determining rates of virus production in aquatic systems by the virus reduction approach Resource Report Resource Website |
Markus G. Weinbauer, Janet M. Rowe, and Steven W. Wilhelm | DOI:10.17504/protocols.io.dsp6dm | VERVE Net | The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells due to the decreased abundance of free virus particles. This reoccurrence can be quantified and used to assess production and cell lysis rates. Several modifications of the method are presented and compared. The approaches have great potential for elucidating trends in virus production rates as well as for making generalized estimates of the quantitative effects of viruses on marine microbial communities. | Gainer PJ, Pound HL, Larkin AA, LeCleir GR, DeBruyn JM, Zinser ER, Johnson ZI, Wilhelm SW (2017) Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. PLoS ONE 12(9): e0184371. doi: 10.1371/journal.pone.0184371 | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | https://doi.org/10.1371/journal.pone.0184371 | 1 | 2015 | Markus G. Weinbauer, Janet M. Rowe, and Steven W. Wilhelm 2015. Determining rates of virus production in aquatic systems by the virus reduction approach. protocols.io https://dx.doi.org/10.17504/protocols.io.dsp6dm | 2021-04-15 09:15:39 | |
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Non-Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek2bcye | 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. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ek2bcye | 2021-04-15 09:15:15 | |||
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Separate different viral genome sizes Resource Report Resource Website |
Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder | DOI:10.17504/protocols.io.dy87zv | VERVE Net | For use in "Fingerprinting aquatic virus communities using PFGE" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Separate different viral genome sizes. protocols.io https://dx.doi.org/10.17504/protocols.io.dy87zv | 2021-04-15 09:15:16 | |||
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Autoclave Frankfurter Fiesta Resource Report Resource Website |
Proro, Melted Mint Forums | DOI:10.17504/protocols.io.ea6bahe | VERVE Net | This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here. | , | http://www.meltedmint.com/forum/viewtopic.php?f=7&t=34 | 1 | 2015 | Proro, Melted Mint Forums 2015. Autoclave Frankfurter Fiesta. protocols.io https://dx.doi.org/10.17504/protocols.io.ea6bahe | 2021-04-15 09:15:15 | ||
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Paraformaldehyde (PFA) from Powder Resource Report Resource Website |
Faculty of Medicine Flow Cytometry Facility, U. of Toronto | DOI:10.17504/protocols.io.c5yy7v | VERVE Net, Sullivan Lab | This is a guide to prepare PFA from powder. This is useful for PFA Fixation. | , | http://www.immunology.utoronto.ca/FlowCytometry/protocols/PFA_Fixation.htm?quot;%3EPreparation%20of%20Paraformaldehyde%20Fixative%3C/a%3E%3Cbr%3E%3C/li%3E%3C/ul%3E%3Ch4%3EExternal%20Protocol%20Links:%3C/h4%3E%3Cul%3E%3Cli%3EPurdue%20University:%C3%82%C2%A0%20%3Ca%20title=PurdueProtocols%20href= | 1 | 2016 | Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Paraformaldehyde (PFA) from Powder. protocols.io https://dx.doi.org/10.17504/protocols.io.c5yy7v | 2021-04-15 09:15:17 | ||
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Prophage Induction in Natural Populations of Heterotrophic Bacteria Resource Report Resource Website |
John H. Paul and Markus Weinbauer | DOI:10.17504/protocols.io.dn95h5 | VERVE Net | This protocol gives two methods for prophage induction in heterotrophic bacterioplankton; one with no viral reduction and the other with viral reduction (see guidelines).Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_030.pdf | 1 | 2015 | John H. Paul and Markus Weinbauer 2015. Prophage Induction in Natural Populations of Heterotrophic Bacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.dn95h5 | 2021-04-15 09:15:45 | ||
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CviRI Buffer B Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.esxbefn | VERVE Net | For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Buffer B. protocols.io https://dx.doi.org/10.17504/protocols.io.esxbefn | 2021-04-15 09:15:45 | ||||
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Adsorption of phage to cyanobacteria Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dq95z5 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Several methods have been presented by Adams (1959) to determine adsorption kinetics of bacteriophages. One way to measure the adsorption efficiency of cyanophages is to assay for free unadsorbed phages (Suttle and Chan 1993). The principle of this assay is to add a known quantity of viruses to host cells (e.g., at an MOI = 0.01 to 0.1). Over a period of 1 to 2 h, small subsamples of the virus:host solution are removed ca. every 15 min and diluted 100-fold to stop further adsorption. The host is then separated from free viruses by centrifugation, and the number of free viruses remaining in the supernatant determined by plaque or end-point dilution assays. A plot of the abundance of free viruses remaining in solution as a function of time should produce a straight line. The slope of this line is then used to calculate the adsorption rate.This procedure can be adapted for other host–virus systems. The example given is for host BBC1 and cyanophage BBC1-P1 (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. Adsorption of phage to cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.dq95z5 | 2021-04-15 09:15:18 | ||
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Protocol for Pulsed Field Gel Electrophoresis Resource Report Resource Website |
John Griffith | DOI:10.17504/protocols.io.dmf43m | VERVE Net, Fuhrman Lab | Fuhrman Lab | 1 | 2015 | John Griffith 2015. Protocol for Pulsed Field Gel Electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.dmf43m | 2021-04-15 09:15:20 | ||||
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10X MOPS Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.etgbejw | VERVE Net | For use in Preparation of Denaturing Agarose Gel for RNA Analysis. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. 10X MOPS Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.etgbejw | 2021-04-15 09:15:19 | ||||
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Barcode Oligos for Linker Amplified DNA Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddp25m | VERVE Net, Sullivan Lab | Sequence for barcoded oligos for linker amplified libraries. Numbers 1 to 29 were developed at the Tucson Marine Phage Lab dervied from MID 1 to 14 recommended by Roche. | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Barcode Oligos for Linker Amplified DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.ddp25m | 2021-04-15 09:15:19 | |||
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Viruses from Hypersaline Waters Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.dph5j5 | 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. Viruses from Hypersaline Waters. protocols.io https://dx.doi.org/10.17504/protocols.io.dph5j5 | 2021-04-15 09:15:22 | ||
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Digestion Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.dek3cv | VERVE Net, Sullivan Lab | For use in the "FASP Kit Protocol-ORNL Developed for Bacteriophage" | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Kristin Corrier/Nathan VerBerkmoes 2016. Digestion Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dek3cv | 2021-04-15 09:15:23 | |||
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Proteinase K Solution Resource Report Resource Website |
DeLong Lab | DOI:10.17504/protocols.io.djf4jm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | DeLong Lab 2015. Proteinase K Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.djf4jm | 2021-04-15 09:15:25 | ||||
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Base agar plates Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dp75rm | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | For use in "Isolation of cyanophages by plaque assays" | 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. Base agar plates. protocols.io https://dx.doi.org/10.17504/protocols.io.dp75rm | 2021-04-15 09:15:27 | |||
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Thanksgiving Dinner Autoclave Style Resource Report Resource Website |
Priorclave | DOI:10.17504/protocols.io.ea9bah6 | VERVE Net | This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.Timing is everything when preparing a large meal. Unfortunately, for the truly epic holiday meals – like Thanksgiving – there never seems to be enough oven space to ensure everything arrives at the table steaming. Something has always cooled, collapsed, or coagulated before the turkey is ready to carve.This is where the autoclave comes in: It’s built to hold loads at around 250 degrees Fahrenheit, and since it subjects them to twice normal atmospheric pressure, it tends to cut cooking times in half. Autoclave cook-time for a small to mid-sized turkey should be less than 2 hours.Wanna impress the in-laws this year? Bring home your favorite tabletop food-grade autoclave (not your Priorclave, though; those are research-grade autoclaves!) and put it to use on the big day. | University of Arizona | http://priorclavena.com/thanksgiving-dinner-autoclave-style/ | 1 | 2016 | Priorclave 2016. Thanksgiving Dinner Autoclave Style. protocols.io https://dx.doi.org/10.17504/protocols.io.ea9bah6 | 2021-04-15 09:15:26 | ||
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SYBR Green or Gold Staining Resource Report Resource Website |
Forest Rohwer | DOI:10.17504/protocols.io.c7sznd | VERVE Net, Sullivan Lab | This protocol is based on RT Noble and JA Fuhrman (1998) Aquatic Microbial Ecology 12:113-118: Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Forest Rohwer 2016. SYBR Green or Gold Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.c7sznd | 2021-04-15 09:15:25 |
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