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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. Non-Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.der3d5 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. RNA Samples Steps. protocols.io dx.doi.org/10.17504/protocols.io.dev3e5 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.Quality trimming of reads is important!
Proper citation: Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.eygbftw Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Pseudoalteromonas Media Recipes. protocols.io dx.doi.org/10.17504/protocols.io.ek6bcze Copy
Authors: Seth John, Bonnie Poulos, Christine Schirmer
Group: VERVE Net, Sullivan Lab
Summary: This protocol describes a technique to recover viruses from natural waters using iron- based flocculation and large-pore-size filtration, followed by resuspension of virus- containing precipitates in a pH 6.5 buffer. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered if using oxalic acid in the resuspension buffer. Particles lose infectivity if resuspended with ascorbic acid in the buffer.
Proper citation: Seth John, Bonnie Poulos, Christine Schirmer 2015. Iron Chloride Precipitation of Viruses from Seawater. protocols.io dx.doi.org/10.17504/protocols.io.c2wyfd Copy
Authors: Natalie Solonenko, Marie Burris
Group: Sullivan Lab
Summary: This protocol details steps to prepare DNA for long-read library prep, including clean-up and shearing.
Proper citation: Natalie Solonenko, Marie Burris 2020. Preparation of extracted DNA for long-read library prep. protocols.io dx.doi.org/10.17504/protocols.io.6iyhcfw Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Jennifer Brum 2016. FVIC (Frequency of Visibly Infected Cells) Protocol. protocols.io dx.doi.org/10.17504/protocols.io.dbp2mm 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 dx.doi.org/10.17504/protocols.io.dde23d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Colony PCR Protocol. protocols.io dx.doi.org/10.17504/protocols.io.c6czav Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of trace metal stock solutions for cyanobacteria trace metal mixture (CTMM)
Proper citation: Matthew Sullivan Lab 2015. Primary trace metal stocks. protocols.io dx.doi.org/10.17504/protocols.io.c8hzt5 Copy
Authors: Faculty of Medicine Flow Cytometry Facility, U. of Toronto
Group: VERVE Net, Sullivan Lab
Summary: This is a guide to prepare PFA from powder. This is useful for PFA Fixation.
Proper citation: Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Paraformaldehyde (PFA) from Powder. protocols.io dx.doi.org/10.17504/protocols.io.c5yy7v Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. SYBR Gold working solutions. protocols.io dx.doi.org/10.17504/protocols.io.c7azid Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Cellulophaga Media Recipes. protocols.io dx.doi.org/10.17504/protocols.io.dez3f5 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 dx.doi.org/10.17504/protocols.io.ddf23m Copy
Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in 'FASP Kit Protocol-ORNL Developed for Bacteriophage'
Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Urea Solution. protocols.io dx.doi.org/10.17504/protocols.io.dei3cd Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Bonnie Poulos 2016. Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.ek3bcyn Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. g20 (myovirus) PCR Protocol. protocols.io dx.doi.org/10.17504/protocols.io.dam2c5 Copy
Authors: Matt Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matt Sullivan Lab 2016. Preparation of Tara Sample DNA From Iron-Chloride Precipitates. protocols.io dx.doi.org/10.17504/protocols.io.c24ygv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Marine Basal Media. protocols.io dx.doi.org/10.17504/protocols.io.dcc2sv Copy
Authors: Marie Burris, Natalie Solonenko, Olivier Zablocki, Ben Temperton
Group: Sullivan Lab
Proper citation: Marie Burris, Natalie Solonenko, Olivier Zablocki, Ben Temperton 2020. Long Read Viromics Amplification Library Preparation (VirION 2). protocols.io dx.doi.org/10.17504/protocols.io.5yug7ww Copy
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