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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   

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Authors: Susan A. Kimmance and Corina P. D. Brussaard
Group: VERVE Net
Summary: The modified dilution assay aims to partition phytoplankton mortality into virus- versus grazing-induced fractions and has previously been applied to several different environments to determine viral lysis rates of natural phytoplankton. The method involves creating a gradient of both grazing and viral lysis by dilution with different proportions of grazer- and virus-free filtrate, and assessing the subsequent impact on phytoplankton growth rates.Kimmance, S. A., and C. P. D. Brussaard. 2010. Estimation of viralinduced phytoplankton mortality using the modified dilution method, p. 65–73. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.

Proper citation: Susan A. Kimmance and Corina P. D. Brussaard 2016. Estimation of viral-induced phytoplankton mortality using the modified dilution method. protocols.io https://dx.doi.org/10.17504/protocols.io.dpf5jm Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to plot MEGAN taxonomic assignments. 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 R9: Plotting Microbial Taxonomy from MEGAN. protocols.io https://dx.doi.org/10.17504/protocols.io.ejdbci6 Copy   

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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   

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Authors: Hannigan GD, Grice EA, et al.
Group: VERVE Net, Club Grice
Summary: This protocol provides methods for quality control of metagenomic data. Included is adapter trimming, quality trimming, decontamination, negative control removal, and pre-processing results. Based on the methods found in 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 P1: Pre-Processing Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.edrba56 Copy   

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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   

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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   

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Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Bambus2 is a scaffolding module that can be applicable to metagenomics settings. MetaVelvet uses a novel graph splitting algorithm during contiging process, and uses the scaffolding module of Velvet (RockBand and Pebble) during scaffolding process. Alternatively, users can output MetaVelvet contigs and uses Bambus2 scaffolding module instead of using RockBand and Pebble.

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Use Bambus2 scaffolding module. protocols.io https://dx.doi.org/10.17504/protocols.io.d7n9md Copy   

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Authors: Bonnie Hurwitz
Group: VERVE Net, Hurwitz Lab, ABE487_HMP, ABE487_EMP
Summary: This tutorial covers a full QIIME workflow using Illumina sequencing data and was adapted from a tutorial on the QIIME website.. This tutorial is intended to be quick to run, and as such, uses only a subset of a full Illumina Genome Analyzer II (GAIIx) run. We'll make use of the Greengenes reference OTUs, which is the default reference database used by QIIME. You can determine which version of Greengenes is being used by running print_qiime_config.py. This will be Greengenes, unless you've configured QIIME to use a different reference database by default.The data used in this tutorial are derived from the Moving Pictures of the Human Microbiome study, where two human subjects collected daily samples from four body sites: the tongue, the palm of the left hand, the palm of the right hand, and the gut (via fecal samples obtained by swapping used toilet paper). These data were sequenced using the barcoded amplicon sequencing protocol described in Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. A more recent version of this protocol that can be used with the Illumina HiSeq 2000 and MiSeq can be found here.

Proper citation: Bonnie Hurwitz 2015. QIIME:Moving Pictures of the human microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.d5288d Copy   

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Authors: Benjamin Tully
Group: VERVE Net, ECOGEO
Summary: This protocol details the use of various unix commands commonly used in bioinformatics.

Proper citation: Benjamin Tully 2016. Unix and Bioinformatics. protocols.io https://dx.doi.org/10.17504/protocols.io.eptbdnn Copy   

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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   

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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   

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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   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. Stacking gel buffer (4X). protocols.io https://dx.doi.org/10.17504/protocols.io.eq4bdyw Copy   

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Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology

Proper citation: André M. Comeau and Rachel T. Noble 2016. FLV tracer assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dzu76v Copy   

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Authors: Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman
Group: VERVE Net, Fuhrman Lab
Summary: The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously. The method is from:Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA.Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat Protoc. 2007;2(2):269-76.Please see the full manuscript for more details.

Proper citation: Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman 2018. Virus and bacteria counts by epifluorescence microscopy with SYBR Green. protocols.io https://dx.doi.org/10.17504/protocols.io.r2dd8a6 Copy   

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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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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Chlorovirus DNA Miniprep Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.erzbd76 Copy   

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Authors: Ms Alex Aitken
Group: VERVE Net, Sullivan Lab
Summary: TE is a commonly used buffer solution in molecular biology, especially in procedures involving DNA or RNA. "TE" is derived from its components: Tris, a common pH buffer, and EDTA, a molecule that chelates cations like Mg2+. The purpose of TE buffer is to solubilize DNA or RNA, while protecting it from degradation: 10 mM Tris, bring to pH 8.0 with HCl, 1 mM EDTA

Proper citation: Ms Alex Aitken 2016. TE Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5uy6v Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to generate input files for CoNet for the phage-bacteria network. 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 R15: CoNet Analysis - Formatting Relative Abundance Files. protocols.io https://dx.doi.org/10.17504/protocols.io.ejpbcmn Copy   

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