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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 https://dx.doi.org/10.17504/protocols.io.c5vy65 Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. g20 (myovirus) PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dam2c5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Marine Basal Media. protocols.io https://dx.doi.org/10.17504/protocols.io.dcc2sv 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 https://dx.doi.org/10.17504/protocols.io.ek3bcyn Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dfr3m5 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 https://dx.doi.org/10.17504/protocols.io.ev8be9w Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Version 3This protocol describes the use of Cesium Chloride to purify viruses with an optional dialysis step to remove the CsCl. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012.References:Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 15(5), 1428–1440. doi:10.1111/j.1462-2920.2012.02836.x.
Proper citation: Matthew Sullivan 2016. Cesium Chloride Dialysis for Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.c7jzkm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For use in the protocol "Large Volume Marine Cyanophage protocols"
Proper citation: Matthew Sullivan 2016. Microbubbling technique. protocols.io https://dx.doi.org/10.17504/protocols.io.egkbbuw Copy
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 https://dx.doi.org/10.17504/protocols.io.dar2d5 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 https://dx.doi.org/10.17504/protocols.io.c7fzjm Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Proper citation: Jennifer Brum 2016. SYBR Staining - Jenn's Method. protocols.io https://dx.doi.org/10.17504/protocols.io.c63zgm 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 https://dx.doi.org/10.17504/protocols.io.dep3dm 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/SDS Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.deh3b5 Copy
Authors: Virginia Rich, DeLong Lab
Group: VERVE Net, Sullivan Lab
Summary: As used in Rich, Konstantinidis, and DeLong. 2008. Rich VI., Konstantinidis K., DeLong EF. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. http://www.ncbi.nlm.nih.gov/pubmed/18028413. Environ. Microbiol., 2008 Feb;10(2):506-21. Epub 2007 Nov 19.
Proper citation: Virginia Rich, DeLong Lab 2016. 96-well DNA Extraction Protocol from 25mm 0.2µm filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c4hyt5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For use in "One-step growth curve for Cyanophage"
Proper citation: Matthew Sullivan 2016. Time 0 growth reading using a plate reader. protocols.io https://dx.doi.org/10.17504/protocols.io.dw47gv Copy
Authors: Matthew Sullivan, Sarah Schwenck, Cristina Howard-Varona, Vinh Dang
Group: VERVE Net, Sullivan Lab
Summary: Bacterial viruses (phages) influence global biogeochemical cycles by modulating bacterial mortality, metabolic output and evolution. However, our understanding of phage infections is limited by few methods and environmentally-relevant model systems. Prior work showed that Cellulophaga baltica phage ϕ38:1 infects its original host lytically, and an alternative host either delayed lytically or lysogenically. Here we investigate these infections through traditional and marker-based approaches, and introduce geneELISA for highthroughput examination of phage‒host interactions.
Proper citation: Matthew Sullivan, Sarah Schwenck, Cristina Howard-Varona, Vinh Dang 2016. geneELISA for highthroughput examination of phage?host interactions. protocols.io https://dx.doi.org/10.17504/protocols.io.dmc42v Copy
Authors: Faculty of Medicine Flow Cytometry Facility, U. of Toronto
Group: VERVE Net, Sullivan Lab
Summary: References:Becton Dickinson Immunocytometry Systems Source Book (1989) 2.10 Lanier, L.L., and Warner, N.L. (1981) Paraformaldehyde Fixation of Hematopoietic Cells for Quantitative Flow Cytometry (FACS) Analysis. Journal of Immunological Methods 47, 25C.A. Williams, M.W. Chase, Stabilizes cell membranes and preserves cell morphology. Methods Immunol. Immunochem. New York 5, (1976)
Proper citation: Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Fixing Cells with Paraformaldehyde (PFA). protocols.io https://dx.doi.org/10.17504/protocols.io.c5xy7m 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 https://dx.doi.org/10.17504/protocols.io.c2zyf5 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: One-step growth curves are used to make determinations about the life cycle of a virus on a particular host. By following a virus infection during one life cycle phase of host a growth curve can be constructed and the burst size can be calculated.
Proper citation: Bonnie Poulos 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.eqfbdtn Copy
Authors: Marcia Osburne
Group: VERVE Net, Sullivan Lab
Proper citation: Marcia Osburne 2016. Syn33 g20 PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.dai2cd Copy
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