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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io https://dx.doi.org/10.17504/protocols.io.dpa5id Copy
Authors: Marie Burris, Ben Temperton, Natalie Solonenko
Group: Sullivan Lab, Temperton Lab
Summary: 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.
Proper citation: Marie Burris, Ben Temperton, Natalie Solonenko 2020. VirION 2. protocols.io https://dx.doi.org/10.17504/protocols.io.6q9hdz6 Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses
Proper citation: 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 Copy
Authors: Jonathan King Lab
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Jonathan King Lab 2016. CsCl Step Gradient to Purify Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c4zyx5 Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: Mapping metagenomic reads from Ocean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter.
Proper citation: Benjamin Bolduc 2016. Mapping Metagenomic Reads to Reference Sequences (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.evybe7w Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Artificial Seawater Based AMP1 Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.c9mz45 Copy
Authors: Forest Rohwer
Group: VERVE Net, Sullivan Lab
Summary: 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
Proper citation: Forest Rohwer 2016. Cesium Chloride Protocol for Phage. protocols.io https://dx.doi.org/10.17504/protocols.io.c37yrm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.deq3dv Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Bonnie Poulos 2016. Marine Purity Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.ekrbcv6 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol.
Proper citation: Matthew Sullivan 2016. Non-Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddk24v Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Jennifer Brum 2016. Using ImageJ to Measure Viral Dimensions in Micrographs. protocols.io https://dx.doi.org/10.17504/protocols.io.ddf23m Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Assembling actual reads from the Ocean Sampling Day (2014) using SPAdes, an assembler implemented in Cyverse.
Proper citation: Benjamin Bolduc 2016. Assembling Viral Metagenomic Data with SPAdes (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewrbfd6 Copy
Authors: JB Waterbury & JM Willey
Group: VERVE Net, Sullivan Lab
Summary: Reference: JB Waterbury & JM Willey. Isolation and growth of marine planktonic cyanobacteria. 1988. Methods in Enzymology 167: 100-105.
Proper citation: JB Waterbury & JM Willey 2016. SN Maintenance Medium for Synechococcus. protocols.io https://dx.doi.org/10.17504/protocols.io.c9hz35 Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: 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.
Proper citation: Benjamin Bolduc 2018. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.wijfccn Copy
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