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Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with high concentrations of viruses. For natural samples, use the protocol “Quantitatively Depositing Viruses onto TEM Grids using an Airfuge”.Note: If purification of the viruses is necessary, refer to Ackermann and Heldal (2010) for various options.
Proper citation: Jennifer Brum 2016. Adsorbing Viruses on TEM Grids. protocols.io dx.doi.org/10.17504/protocols.io.dar2d5 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.ek4bcyw Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Case 2: Fix samples. Use this protocol when long term storage of slide is required.For when you can count your samples in a few days, see Case 1.
Proper citation: Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 2). protocols.io dx.doi.org/10.17504/protocols.io.c7fzjm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.dep3dm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Titration of AmPure XP Beads for Removal of Fragments . protocols.io dx.doi.org/10.17504/protocols.io.c52y8d Copy
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 dx.doi.org/10.17504/protocols.io.dpa5id Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: 10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol.
Proper citation: Matthew Sullivan Lab 2015. 10g/L Fe Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.c2zyf5 Copy
Authors: Rex Malmstrom
Group: VERVE Net, Sullivan Lab
Summary: This is a storage solution that stabilizes and protectsRNA while inactivating RNase
Proper citation: Rex Malmstrom 2015. RNAlater Recipe. protocols.io dx.doi.org/10.17504/protocols.io.c56y9d Copy
Authors: Jonathan King
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used in the CsCl Step Gradient to Purify Phage Protocol
Proper citation: Jonathan King 2016. CsCl Step Gradient Buffer. protocols.io dx.doi.org/10.17504/protocols.io.dmj44m Copy
Authors: Benjamin Bolduc
Group: VERVE Net, 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 2019. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.x5xfq7n Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This method for the enumeration of aquatic viruses is a low-cost alternative to the commonly used filter-mount method. Briefly, fluorescently-stained samples are wetmounted directly onto slides for epifluorescence microscopy after an optional chemical flocculation concentration step used for samples with anticipated virus concentrations of 7 viruses mL-1 (samples with >5×107 viruses mL-1 do not require this concentration step prior to analysis). Virus concentration in the wet-mounted sample is determined from the ratio of viruses to microsphere beads, which are added at a known concentration. This wet-mount method for enumerating viruses is significantly less expensive than the filter-mount method (i.e., the cost of microsphere beads per sample is ~500-fold lower than the cost of one filter per sample), and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations encountered in field and laboratory samples. The only limitation of this method is that samples with virus concentrations ≤1×106 viruses mL-1 cannot be enumerated, as the abundance of viruses is too low for efficient enumeration.Figure 1. Overview of the 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. Wet-mount Method for Enumeration of Aquatic Viruses. protocols.io dx.doi.org/10.17504/protocols.io.c8pzvm Copy
Authors: Natalie Solonenko
Group: Sullivan Lab
Summary: Now includes media used for phosphate limitation experiments.
Proper citation: Natalie Solonenko 2016. Pseudoalteromonas Media Recipes. protocols.io dx.doi.org/10.17504/protocols.io.fz4bp8w Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Supplement to seawater for growth of cyanobacteria.
Proper citation: Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm Copy
Authors: Ms Alex Aitken
Group: VERVE Net, Sullivan Lab
Summary: This shows how to make 1M Tris.
Proper citation: Ms Alex Aitken 2016. 1M Tris. protocols.io dx.doi.org/10.17504/protocols.io.c5vy65 Copy
Authors: Natalie Solonenko, Marie Burris
Group: Sullivan Lab, Temperton Lab
Summary: This protocol is intended for extraction of HMW DNA from bacterial or viral samples.
Proper citation: Natalie Solonenko, Marie Burris 2019. DNA extraction for HMW DNA. protocols.io dx.doi.org/10.17504/protocols.io.6cbhasn Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
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 2016. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.ev8be9w Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io dx.doi.org/10.17504/protocols.io.dfr3m5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.dem3c5 Copy
Authors: Marine Phage Lab, Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Version 1b17 October 2012This protocol decribes the extraction of DNA from viral particles using Wizard Prep Resin and Columns from Promega.
Proper citation: Marine Phage Lab, Matthew Sullivan Lab 2016. DNA Extraction of Cesium Chloride-Purified Viruses using Wizard Prep Columns. protocols.io dx.doi.org/10.17504/protocols.io.c26yhd Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Identifying putative viral sequences from SPAdes-assembled data from the Ocean Sampling Day (2014) metagenomic datasets using VirSorter.
Proper citation: Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.eyjbfun Copy
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