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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Iodoacetamide Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.dej3cm | 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. Iodoacetamide Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dej3cm | 2021-04-15 09:14:43 | |||
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DNA Extraction Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c32yqd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA Extraction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c32yqd | 2021-04-15 09:14:43 | ||||
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DNase I Treatment Resource Report Resource Website |
James E. Thornton | DOI:10.17504/protocols.io.c3myk5 | VERVE Net, Sullivan Lab, Culley Lab_ULaval | This protocol describes the preparation of and treatment with DNase I to degrade DNA in solutions containing iron chloride, EDTA–Mg ascorbate buffer, and cesium chloride. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012. We use this protocol primarily to remove free host and other contaminating DNA from phage preparations prior to extracting nucleic acid from the phage particles. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | James E. Thornton 2015. DNase I Treatment. protocols.io https://dx.doi.org/10.17504/protocols.io.c3myk5 | 2021-04-15 09:14:41 | |||
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Iron Chloride Solution Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c8wzxd | 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. Iron Chloride Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c8wzxd | 2021-04-15 09:15:00 | |||
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Soil viral extraction protocol for ssDNA & dsDNA viruses Resource Report Resource Website |
Gary Trubl, Natalie Solonenko, Yueh-Fen Li | DOI:10.17504/protocols.io.tzzep76 | Sullivan Lab | Protocol for resuspending viruses from soils and sediments. See attached file for considerations, adaptations, and references. This version does not include CsCl purification, see version 2 for CsCl information. | Trubl G, Roux S, Solonenko N, Li Y, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB, Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. PeerJ doi: 10.7717/peerj.7265 | Ohio State University, Columbus, Ohio State University, Columbus, Ohio State University, Columbus | https://doi.org/10.7717/peerj.7265 | 3 | 2018 | Gary Trubl, Natalie Solonenko, Yueh-Fen Li 2018. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.tzzep76 | 2021-04-15 09:14:46 | |
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CsCl purified phage lysate, Proteinase K, SDS Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c68zhv | VERVE Net, Sullivan Lab | This mixture is used for the DNA Extraction Protocol. | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. CsCl purified phage lysate, Proteinase K, SDS. protocols.io https://dx.doi.org/10.17504/protocols.io.c68zhv | 2021-04-15 09:14:45 | |||
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DNA/RNA Extractions from Sterivex Filters Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c4bysm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA/RNA Extractions from Sterivex Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c4bysm | 2021-04-15 09:14:49 | ||||
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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.ewabfae | 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, 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. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewabfae | 2021-04-15 09:14:51 | |
|
Isotopic Labeling of Cyanobacteria and DNA Analysis Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.c9nz5d | VERVE Net, Sullivan Lab | Protocol for labeling bacteria with N15. The bacterial DNA was made “heavy” so that community viral and host bacterial DNA could be distinguished from each other after sorting by using density gradient centrifugation. | Matthew Sullivan Lab | 1 | 2016 | Bonnie Poulos 2016. Isotopic Labeling of Cyanobacteria and DNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.c9nz5d | 2021-04-15 09:15:20 | |||
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FVIC (Frequency of Visibly Infected Cells) Protocol Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dbp2mm | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly infected cells (FVIC), the frequency of infected cells (FIC), the fraction of mortality due to viral lysis (FMVL), and burst size. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. FVIC (Frequency of Visibly Infected Cells) Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dbp2mm | 2021-04-15 09:15:20 | |||
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0.5M EDTA Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5wy7d | VERVE Net, Sullivan Lab | This shows how to make 0.5M EDTA | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c5wy7d | 2021-04-15 09:14:56 | |||
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Extracting Bacterial DNA from filters Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.qv8dw9w | Sullivan Lab, Gene Flow in Subzero Brines | Adapted from Tara Oceans extraction protocol (see citation). | The Ohio State University | 1 | 2018 | Natalie Solonenko 2018. Extracting Bacterial DNA from filters. protocols.io https://dx.doi.org/10.17504/protocols.io.qv8dw9w | 2021-04-15 09:15:27 | |||
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Resuspension Buffer P1 Resource Report Resource Website |
Qiagen | DOI:10.17504/protocols.io.hxgb7jw | VERVE Net, Sullivan Lab | This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A | Matthew Sullivan Lab, University of Arizona, The Ohio State University | http://people.mbi.ucla.edu/sumchan/qiagenbuffer.html | 2 | 2017 | Qiagen 2017. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.hxgb7jw | 2021-04-15 09:15:30 | ||
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16S PCR Universal Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.c5my45 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Natalie Solonenko 2016. 16S PCR Universal. protocols.io https://dx.doi.org/10.17504/protocols.io.c5my45 | 2021-04-15 09:15:35 | ||||
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One-Step Growth Curves for Cyanophages Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dan2dd | VERVE Net, Sullivan Lab | Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. One-Step Growth Curves for Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.dan2dd | 2021-04-15 09:15:36 | ||||
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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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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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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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Preparing Data for vContact from Proteins (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ev7be9n | Sullivan Lab | 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: 10.1038/ismej.2016.89 | The Ohio State University | https://doi.org/ismej201689 | 1 | 2016 | Benjamin Bolduc 2016. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ev7be9n | 2021-04-15 09:15:46 | |
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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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