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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Amplification of phage genes from lysates and environmental samples Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.djn4md | VERVE Net, Sullivan Lab | From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.PLOS Biology, 2006 4(8):e234. Please see the published manuscript for additional information. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Amplification of phage genes from lysates and environmental samples. protocols.io https://dx.doi.org/10.17504/protocols.io.djn4md | 2021-04-15 09:16:52 | |||
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Lysozyme & RNase A Solution Resource Report Resource Website |
DeLong Lab | DOI:10.17504/protocols.io.dje4jd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | DeLong Lab 2015. Lysozyme & RNase A Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dje4jd | 2021-04-15 09:17:03 | ||||
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Preparation of Virus DNA from Seawater for Metagenomics Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c28yhv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Matthew Sullivan Lab 2016. Preparation of Virus DNA from Seawater for Metagenomics. protocols.io https://dx.doi.org/10.17504/protocols.io.c28yhv | 2021-04-15 09:17:04 | ||||
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Urea Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.dei3cd | VERVE Net, Sullivan Lab | For use in 'FASP Kit Protocol-ORNL Developed for Bacteriophage' | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Kristin Corrier/Nathan VerBerkmoes 2016. Urea Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dei3cd | 2021-04-15 09:17:07 | |||
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0.7% Agarose Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7bzim | VERVE Net, Sullivan Lab | . | 1 | 2016 | Matthew Sullivan 2016. 0.7% Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.c7bzim | 2021-04-15 09:14:24 | ||||
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Cellulophaga Media Recipes Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dez3f5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.dez3f5 | 2021-04-15 09:14:27 | ||||
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FASP Kit Protocol-ORNL Developed for Bacteriophage Resource Report Resource Website |
Nathan VerBerkmoes | DOI:10.17504/protocols.io.ddn25d | VERVE Net, Sullivan Lab | Collaborator, Nathan VerBerkmoes (Oak Ridge National Labs), worked with Tucson Marine Phage Lab to develop more sensitive proteomics assays for viral isolates which we are now also using for environmental viral concentrates. A new sample prep method (FASP) was optimized to maximize the signal from our commonly low-protein containing samples, and then run using 2d-LC-MS-MS to maximize detection across the large dynamic range in isolate and environmental samples. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Nathan VerBerkmoes 2016. FASP Kit Protocol-ORNL Developed for Bacteriophage. protocols.io https://dx.doi.org/10.17504/protocols.io.ddn25d | 2021-04-15 09:14:23 | |||
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MTN100 with 5x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ded3a5 | VERVE Net, Sullivan Lab | This mixture is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 5x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.ded3a5 | 2021-04-15 09:14:33 | |||
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BG-11 Medium for Freshwater Cyanobacteria Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.ddd225 | VERVE Net, Sullivan Lab | This medium is used successfully for most cyanobacteria. Vitamin B12 may be added for those species that require it. Use f/2 vitamin solution. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. BG-11 Medium for Freshwater Cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.ddd225 | 2021-04-15 09:14:30 | |||
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Cyanophage plaque purification Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c3yypv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. Cyanophage plaque purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3yypv | 2021-04-15 09:14:38 | ||||
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MTN100 with 3x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dee3bd | VERVE Net, Sullivan Lab | This mixture is is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 3x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.dee3bd | 2021-04-15 09:14:28 | |||
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Isolation of DNA from phage lysate Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.c36yrd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Natalie Solonenko 2016. Isolation of DNA from phage lysate. protocols.io https://dx.doi.org/10.17504/protocols.io.c36yrd | 2021-04-15 09:14:46 | ||||
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Quality Control of Reads Using Trimmomatic (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.eygbftw | Sullivan Lab, iVirus | A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.Quality trimming of reads is important! | Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB, iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal 11(1). doi: ismej201689 | The Ohio State University | https://www.nature.com/articles/ismej201689.pdf?origin=ppub | 2 | 2016 | Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eygbftw | 2021-04-15 09:14:51 | |
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Non-Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.der3d5 | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.der3d5 | 2021-04-15 09:14:47 | |||
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Preparation of extracted DNA for long-read library prep Resource Report Resource Website |
Natalie Solonenko, Marie Burris | DOI:10.17504/protocols.io.6iyhcfw | Sullivan Lab | This protocol details steps to prepare DNA for long-read library prep, including clean-up and shearing. | The Ohio State University, The Ohio State University | 1 | 2020 | Natalie Solonenko, Marie Burris 2020. Preparation of extracted DNA for long-read library prep. protocols.io https://dx.doi.org/10.17504/protocols.io.6iyhcfw | 2021-04-15 09:14:55 | |||
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0.5M EDTA Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c58y9v | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c58y9v | 2021-04-15 09:14:53 | ||||
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Pseudoalteromonas Media Recipes Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek6bcze | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.ek6bcze | 2021-04-15 09:14:38 | ||||
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Iron Chloride Precipitation of Viruses from Seawater Resource Report Resource Website |
Seth John, Bonnie Poulos, Christine Schirmer | DOI:10.17504/protocols.io.c2wyfd | VERVE Net, Sullivan Lab | This protocol describes a technique to recover viruses from natural waters using iron- based flocculation and large-pore-size filtration, followed by resuspension of virus- containing precipitates in a pH 6.5 buffer. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered if using oxalic acid in the resuspension buffer. Particles lose infectivity if resuspended with ascorbic acid in the buffer. | 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 | 2015 | Seth John, Bonnie Poulos, Christine Schirmer 2015. Iron Chloride Precipitation of Viruses from Seawater. protocols.io https://dx.doi.org/10.17504/protocols.io.c2wyfd | 2021-04-15 09:14:39 | |||
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Buffered glutaraldehyde Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7gzjv | VERVE Net, Sullivan Lab | Formulation for a phosphate-buffered 20% glutaraldehyde stock solution. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Li Deng 2015. Buffered glutaraldehyde. protocols.io https://dx.doi.org/10.17504/protocols.io.c7gzjv | 2021-04-15 09:14:56 | |||
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Calculating burst size Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddm245 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Calculating burst size. protocols.io https://dx.doi.org/10.17504/protocols.io.ddm245 | 2021-04-15 09:14:42 |
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