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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Assembling Viral Metagenomic Data with SPAdes (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.evzbe76 | Sullivan Lab | Assembling actual reads from the Ocean Sampling Day (2014) using SPAdes, an assembler implemented in Cyverse. | 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: 10.1038/ismej.2016.89 | The Ohio State University | https://doi.org/ismej201689 | 1 | 2016 | Benjamin Bolduc 2016. Assembling Viral Metagenomic Data with SPAdes (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.evzbe76 | 2021-04-15 09:15:21 | |
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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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Preparing Data for vContact from Proteins (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.eyhbft6 | Sullivan Lab, iVirus | Preparing data for use in vContact by using VirSorted Ocean Sampling Day (2014) contigs, using tools available in Cyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this protocol are suitable for vContact-PCs. | 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. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eyhbft6 | 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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Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.gwcbxaw | 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. | Bolduc B, Jang HB, Doulcier G, You Z, Roux S, Sullivan MB, vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect and . PeerJ doi: 10.7717/peerj.3243 | The Ohio State University | https://dx.doi.org/10.7717/peerj.3243 | 3 | 2017 | Benjamin Bolduc 2017. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gwcbxaw | 2021-04-15 09:15:27 | |
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Quality Control of Reads Using Trimmomatic (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ewbbfan | Sullivan Lab | 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! | The Ohio State University | 1 | 2016 | Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewbbfan | 2021-04-15 09:15:28 | |||
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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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Phage Buffer Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c5ey3d | VERVE Net, Sullivan Lab | Can be used for diluting or resuspending phage preparations. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2015 | Matthew Sullivan 2015. Phage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5ey3d | 2021-04-15 09:15:37 | |||
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WH7803 PCR Protocol Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.dak2cv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Li Deng 2016. WH7803 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dak2cv | 2021-04-15 09:15:36 | ||||
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Ascorbic-EDTA Buffer Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c8xzxm | VERVE Net, Sullivan Lab | For use in Wet-mount Method for Enumeration of Aquatic Viruses | 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, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Ascorbic-EDTA Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c8xzxm | 2021-04-15 09:15:51 | |||
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One-step growth curves for Pseudoalteromonas phages Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.den3dd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Natalie Solonenko 2016. One-step growth curves for Pseudoalteromonas phages. protocols.io https://dx.doi.org/10.17504/protocols.io.den3dd | 2021-04-15 09:15:49 | ||||
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DNA Precipitation Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c34yqv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c34yqv | 2021-04-15 09:15:48 | ||||
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Marine Purity Broth Resource Report Resource Website |
Bertillson et al. | DOI:10.17504/protocols.io.dcm2u5 | VERVE Net, Sullivan Lab | Purpose: To test axenic cultures for purity | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bertillson et al. 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.dcm2u5 | 2021-04-15 09:15:45 | |||
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1M Sodium citrate Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c6azad | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 1M Sodium citrate. protocols.io https://dx.doi.org/10.17504/protocols.io.c6azad | 2021-04-15 09:15:45 | ||||
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Plaque assay protocol for Cellulophaga Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddg23v | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Plaque assay protocol for Cellulophaga. protocols.io https://dx.doi.org/10.17504/protocols.io.ddg23v | 2021-04-15 09:15:47 | ||||
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Fixation of Planktonic Samples Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3ayid | VERVE Net, Sullivan Lab | Modified after Glöckner et al. 1999 | Matthe Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.c3ayid | 2021-04-15 09:15:55 | |||
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Phage Tangential Flow Filtration Resource Report Resource Website |
Forest Rohwar | DOI:10.17504/protocols.io.c7yzpv | VERVE Net, Sullivan Lab | In tangential flow filtration (TFF), the sample is run parallel to the filter. Particles that are smaller than the pore size are pushed out through the holes (the filtrate). Particles that are larger than the pore size are retained inside the filter (the retentate). TFF is most effective when a reservoir is used so that the sample can be recycled through numerous times. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Forest Rohwar 2016. Phage Tangential Flow Filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.c7yzpv | 2021-04-15 09:16:00 | |||
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Plaque Assay Protocol for Pseudoalteromonas Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.de33gm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Natalie Solonenko 2016. Plaque Assay Protocol for Pseudoalteromonas. protocols.io https://dx.doi.org/10.17504/protocols.io.de33gm | 2021-04-15 09:16:04 | ||||
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DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns Resource Report Resource Website |
Marine Phage Lab, Matthew Sullivan Lab | DOI:10.17504/protocols.io.c26yhd | VERVE Net, Sullivan Lab | Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega. | Matthew Sullivan Lab, University of Arizona, Ohio State University, Matthew Sullivan Lab, University of Arizona, Ohio State University | http://www.eebweb.arizona.edu/faculty/mbsulli/protocols/protocols/Wizard_Column_Viral_DNA_Extraction_v1.pdf | 1 | 2016 | Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io https://dx.doi.org/10.17504/protocols.io.c26yhd | 2021-04-15 09:15:59 | ||
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Pseudoalteromonas Media Recipes Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.de23gd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.de23gd | 2021-04-15 09:16:04 |
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