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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   

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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   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Phenol extraction of Chlorella cells. protocols.io https://dx.doi.org/10.17504/protocols.io.eshbeb6 Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride. protocols.io https://dx.doi.org/10.17504/protocols.io.eq7bdzn Copy   

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Authors: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: This tutorial demonstrates the use of VIROME for comparing viral metagenome libraries analyzed with the VIROME pipeline as well as comparative analysis of viral communities using the Quantitative Insights in Microbial Ecology package (QIIME). Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information.

Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. Comparative metagenomic analysis using VIROME. protocols.io https://dx.doi.org/10.17504/protocols.io.d7j9km Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines how to generate tables to analyze CRISPR interactions. Based on methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R16: CRISPR Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejqbcmw Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "One-step growth experiments (cyanophages)"

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Remove unadsorbed phages. protocols.io https://dx.doi.org/10.17504/protocols.io.drb52m Copy   

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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   

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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   

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Authors: HANNIGAN GC, GRICE EA, ET AL
Group: VERVE Net, Club Grice
Summary: This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods based on the publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: HANNIGAN GC, GRICE EA, ET AL 2016. Script P3: Open Reading Frame Prediction. protocols.io https://dx.doi.org/10.17504/protocols.io.efpbbmn Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on Synechococcus sp. BBC1 (Suttle and Chan 1993).

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. One-step growth experiments (cyanophages). protocols.io https://dx.doi.org/10.17504/protocols.io.dra52d Copy   

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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   

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Authors: Ken Stedman
Group: VERVE Net
Summary: For use in "PCTE Protocol for VLP enumeration"

Proper citation: Ken Stedman 2016. PCTE filter staining. protocols.io https://dx.doi.org/10.17504/protocols.io.eavbae6 Copy   

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Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: The following methods are basically method “A” of Zillig et al. (1994) and were described recently in detail by Prangishvili (2006). These methods consist of enrichment cultures followed by host isolation and screening for virus production in both these isolates and enrichment cultures. These techniques are very similar to those used for bacteriophages, with the major exception being the extreme growth conditions (80˚C, pH 3).This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information.

Proper citation: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2015. Viruses from Sulfolobus and close relatives. protocols.io https://dx.doi.org/10.17504/protocols.io.dpb5im Copy   

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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   

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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   

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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. PCR amplification of the SISPA primer reaction mixture. protocols.io https://dx.doi.org/10.17504/protocols.io.emebc3e Copy   

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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 https://dx.doi.org/10.17504/protocols.io.dar2d5 Copy   

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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   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R5: Virome Alpha Diversity. protocols.io https://dx.doi.org/10.17504/protocols.io.eimbcc6 Copy   

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