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Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
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.eyibfue Copy
Authors: Gary Trubl, Natalie Solonenko
Group: Sullivan Lab
Summary: Protocol for resuspending viruses from soils and sediments.
Proper citation: Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.hvxb67n Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to negatively or positively stain viruses that have been deposited onto TEM grids so that they can be imaged using transmission electron microscopy (TEM). Positive staining stains the virus itself such that the virus is dark against a lighter background (Figure 1A). This is the easiest staining to do and yields results suitable for analyzing the morphological diversity of viruses from aquatic samples. Negative staining relies on some stain remaining around the edges of a virus such that the details of the virus are clearly defined (Figure 1B). Negative staining is more difficult and is used to obtain publication quality micrographs of viruses.Note: To deposit viruses onto the grids prior to staining, use either the “Adsorbing Viruses onto TEM Grids” protocol or the “Quantitatively Depositing Viruses onto TEM Grids” protocol. Grids should be stained immediately after depositing viruses onto them.
Proper citation: Jennifer Brum 2016. Positive and Negative Staining of Viruses on TEM Grids. protocols.io https://dx.doi.org/10.17504/protocols.io.day2fv Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to analyze a natural aquatic virus sample using transmission electron microscopy (TEM). The purpose is to obtain the capsid diameter distributions of the viral assemblage, tail length distributions of the viral assemblage, and percentages of each viral morphotype in a sample.Note: Prior to using this protocol, deposit viruses from your sample onto a TEM grid using the protocol “Quantitatively Depositing Viruses onto TEM Grids” then stain the viruses using the protocol “Positive and Negative Staining of Viruses on TEM Grids”.
Proper citation: Jennifer Brum 2016. Analysis of Viral Morphological Characteristics. protocols.io https://dx.doi.org/10.17504/protocols.io.dde23d Copy
Authors: Li Deng, Bonnie T. Poulos, Matthew B. Sullivan
Group: VERVE Net, Sullivan Lab
Summary: AbstractOcean viruses are abundant, ubiquitous, and play important roles in global biogeochemical cycles through mortality, horizontal gene transfer and manipulation of host metabolism. However, the ability to link viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. Here, we present viral tagging (VT), a method that combines mixtures of isotope labeled host cells and fluorescent viruses with flow cytometry. In a single experiment, we can screen 107 uncultivated ocean viruses with a single strain of Synechococcus. These viruses can then be sequenced to quantitatively link objectivelydefined environmental viral populations, and their genomes, to their hosts.
Proper citation: Li Deng, Bonnie T. Poulos, Matthew B. Sullivan 2016. Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging. protocols.io https://dx.doi.org/10.17504/protocols.io.c6zzf5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The following are media recipes necessary for isolating and maintaining Synechococcus isolates.
Proper citation: Matthew Sullivan 2016. Media recipes for Synechococcus isolates. protocols.io https://dx.doi.org/10.17504/protocols.io.c9jz4m Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Colony PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6czav Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: 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.
Proper citation: Benjamin Bolduc 2018. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.wigfcbw Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. YTSS Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbq2mv Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. SYBR Gold working solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.c7azid Copy
Authors: Benjamin Bolduc, Simon Roux
Group: Sullivan Lab, iVirus
Summary: Cluster genomes is script that clusters genomes at a set nucleotide identity and coverage length. Additonally, it offers the ability to cluster sequences whose ends may not align correspondingly, i.e. the special cases of assembled, circular viral genomes that are treated as 'linear' by other sequence-clustering software (that can "miss" the ends).This is 'beta-like' software that has been vetted, though has not been as thoroughly tested as other widely-recognized clustering tools, such as CD-HIT, UCLUST, etc... As with all software, please examine the final results to see if they make sense.
Proper citation: Benjamin Bolduc, Simon Roux 2017. Clustering Viral Genomes in iVirus. protocols.io https://dx.doi.org/10.17504/protocols.io.gwebxbe Copy
Authors: Li Deng & Jennifer Brum
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng & Jennifer Brum 2016. SYBR Gold Staining for viral enumeration using 13 mm Anodisc 0.02 ?m filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c7cziv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Last optimized January 2006, updated by Matt on March 16 2009
Proper citation: Matthew Sullivan 2016. Large Volume Marine Cyanophage Phage Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3iykd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. FISH Protocol for FISH & FLOW. protocols.io https://dx.doi.org/10.17504/protocols.io.dfe3jd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for Viruses (See guidelines for DNA Extraction).
Proper citation: Matthew Sullivan 2016. Cesium Chloride Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.c7dzi5 Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
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 https://dx.doi.org/10.17504/protocols.io.ev2be8e Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol.
Proper citation: Matthew Sullivan 2016. Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddj24m Copy
Authors: Adriana Alberti
Group: VERVE Net, Sullivan Lab
Summary: Protocol for preparation of short single and paired-end libraries from genomic dsDNA starting from low DNA quantity (up to 10 ng) for Illumina sequenincg. Developed by Adriana Alberti at Genoscope.
Proper citation: Adriana Alberti 2016. Low input Library Preparation for Illumina Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.ddq25v Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Host Range Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.dew3fd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses
Proper citation: Matthew Sullivan 2016. Working Bead Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c84zyv Copy
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