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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cellulophaga growth reading Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dpa5id | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io https://dx.doi.org/10.17504/protocols.io.dpa5id | 2021-04-15 09:16:31 | |||
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VirION 2 Resource Report Resource Website |
Marie Burris, Ben Temperton, Natalie Solonenko | DOI:10.17504/protocols.io.6q9hdz6 | Sullivan Lab, Temperton Lab | This collection contains protocols for the extraction and preparation of DNA for long-read work and library amplification of long reads from microbial or viral DNA. | The Ohio State University, University of Exeter, The Ohio State University | 1 | 2020 | Marie Burris, Ben Temperton, Natalie Solonenko 2020. VirION 2. protocols.io https://dx.doi.org/10.17504/protocols.io.6q9hdz6 | 2021-04-15 09:16:56 | |||
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SYBR Gold Working Stock Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c82zyd | 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. SYBR Gold Working Stock. protocols.io https://dx.doi.org/10.17504/protocols.io.c82zyd | 2021-04-15 09:16:36 | |||
|
CsCl Step Gradient to Purify Phage Resource Report Resource Website |
Jonathan King Lab | DOI:10.17504/protocols.io.c4zyx5 | VERVE Net, Sullivan Lab | April 2000 chpPhage are best purified by a CsCl gradient. This is separated by density not sedimentation as in a sucrose gradient.This is a protocol for P22 like phage not T4 with delicate tail fibers. | Jonathan King Lab, MIT | http://web.mit.edu/king-lab/www/cookbook/cscl_grad_phage.htm | 1 | 2016 | Jonathan King Lab 2016. CsCl Step Gradient to Purify Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c4zyx5 | 2021-04-15 09:16:45 | ||
|
Mapping Metagenomic Reads to Reference Sequences (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.evybe7w | Sullivan Lab | Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter. | The Ohio State University | 1 | 2016 | Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.evybe7w | 2021-04-15 09:17:00 | |||
|
Artificial Seawater Based AMP1 Medium Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.c9mz45 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Artificial Seawater Based AMP1 Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.c9mz45 | 2021-04-15 09:16:48 | ||||
|
Cesium Chloride Protocol for Phage Resource Report Resource Website |
Forest Rohwer | DOI:10.17504/protocols.io.c37yrm | VERVE Net, Sullivan Lab | This protocol contains 4 sections: 1. Cesium Chloride Gradient to separate phage from bacteria. Marine viruses around 1.5g/ml 2. DNase I treatment of CsCl-purified phage 3. Formamide Extraction of DNA from phagE4. 4. CTAB | Matthew Sullivan Lab | 1 | 2016 | Forest Rohwer 2016. Cesium Chloride Protocol for Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c37yrm | 2021-04-15 09:17:01 | |||
|
Media Recipes Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.deq3dv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.deq3dv | 2021-04-15 09:16:49 | ||||
|
Marine Purity Broth Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ekrbcv6 | VERVE Net, Sullivan Lab | Purpose: To test axenic cultures for purity. Protocol described in S. Bertillson, O. Berglund, D.M. Karl, S.W. Chisholm (2003). Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea. Limnol Oceanogr 48(5):1721-1731. | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.ekrbcv6 | 2021-04-15 09:17:02 | |||
|
Non-Centrifuged Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddk24v | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Non-Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddk24v | 2021-04-15 09:17:04 | |||
|
Using ImageJ to Measure Viral Dimensions in Micrographs Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.ddf23m | VERVE Net, Sullivan Lab | Purpose: This protocol describes the use of ImageJ to measure dimensions of viruses in TEM micrographs, but can be applied to the measurement of anything in any image. The ImageJ program can be downloaded free (http://rsbweb.nih.gov/ij/) and it’s usage should be cited in publications using the reference listed on the website. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Using ImageJ to Measure Viral Dimensions in Micrographs. protocols.io https://dx.doi.org/10.17504/protocols.io.ddf23m | 2021-04-15 09:17:04 | |||
|
Assembling Viral Metagenomic Data with SPAdes (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ewrbfd6 | Sullivan Lab, iVirus | 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: ismej201689 | The Ohio State University | https://www.nature.com/articles/ismej201689.pdf?origin=ppub | 2 | 2016 | Benjamin Bolduc 2016. Assembling Viral Metagenomic Data with SPAdes (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewrbfd6 | 2021-04-15 09:17:06 | |
|
SN Maintenance Medium for Synechococcus Resource Report Resource Website |
JB Waterbury & JM Willey | DOI:10.17504/protocols.io.c9hz35 | VERVE Net, Sullivan Lab | Reference: JB Waterbury & JM Willey. Isolation and growth of marine planktonic cyanobacteria. 1988. Methods in Enzymology 167: 100-105. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | JB Waterbury & JM Willey 2016. SN Maintenance Medium for Synechococcus. protocols.io https://dx.doi.org/10.17504/protocols.io.c9hz35 | 2021-04-15 09:17:06 | |||
|
Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.wijfccn | 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. | The Ohio State University | https://dx.doi.org/10.7717/peerj.3243 | 4 | 2018 | Benjamin Bolduc 2018. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.wijfccn | 2021-04-15 09:17:08 |
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