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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: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Preparation of Denaturing Agarose Gel for RNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.es4begw 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: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. NC64A virus purification. protocols.io https://dx.doi.org/10.17504/protocols.io.etebeje 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: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.er4bd8w 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: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Isolation of cyanophages by liquid bioassays"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Phytoplankton and bacteria filtration. protocols.io https://dx.doi.org/10.17504/protocols.io.dp55q5 Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Chlorella NC64A and Mictractinium Pbi virus Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.etfbejn Copy
Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviJI Storage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.esnbede Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Methyltransferase Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.etjbekn Copy
Authors: KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN
Group: VERVE Net
Summary: For use in Generating viral metagenomes from the coral holobiont.
Proper citation: KAREN D. WEYNBERG, ELISHA M. WOOD-CHARLSON, CURTIS A. SUTTLE, AND MADELEINE J. H. VAN OPPEN 2016. Reconditioning PCR amplification of the SISPA primer denaturing cycles. protocols.io https://dx.doi.org/10.17504/protocols.io.emgbc3w Copy
Authors: Stanton Burnton, Carolina Cadena, Edmond Dion, Qianwen Luo
Group: VERVE Net
Summary: These protocols were developed to show the features of the protocols.io platform and how groups like VERVE Net can implement future protocol design based from the mock and technical protocols written. Each author wrote one specific protocol to model applications of protocols.io and VERVE Net together.
Proper citation: Stanton Burnton, Carolina Cadena, Edmond Dion, Qianwen Luo 2016. Mock & Technical Protocols for VERVE Net. protocols.io https://dx.doi.org/10.17504/protocols.io.etkbekw Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. One Step Procedure for Screening Recombinant Plasmids by Size. protocols.io https://dx.doi.org/10.17504/protocols.io.ersbd6e 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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