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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Buffer A. protocols.io dx.doi.org/10.17504/protocols.io.eswbefe Copy
Authors: Barbra Ferrell
Group: VERVE Net, Wommack/Polson Viral Ecology and Informatics Resources (VEIL) Lab
Summary: Viral Informatics Resource for Metagenome Exploration (VIROME) is a bioinformatics pipeline that classifies viral metagenome sequences after searching against annotated reference sequence databases (i.e., UniRef, SEED, ACLAME, COG, GO, KEGG, and PhageSEED) and a custom environmental database, Metagenomes Online (MgOl). VIROME’s compare tool allows users to compare any number of metagenomes to one another by generating a Biological Observation Matrix (biom) file that contain counts of occurrences of custom observations (comparison metrics), and a mapping text file that provides per-sample metadata (library IDs and descriptions). Quantitative Insights Into Microbial Ecology (QIIME) is an open-source software pipeline that allows users to interpret raw sequencing data and create graphical displays to interact with the data. QIIME is modular, providing users with the flexibility to select and integrate various applications. While QIIME has many capabilities and online tutorials, this SOP is limited to the steps a user will take to use VIROME’s compare tool output (biom and mapping files) to explore composition (what is in a sample), alpha-diversity (diversity within a sample), and beta-diversity (comparison of diversity between samples). This SOP generally follows guidance in online tutorials but with modifications unique to the VIROME Comparinator output analysis.
Proper citation: Barbra Ferrell 2016. QIIME: VIROME comparinator tool diversity metrics. protocols.io dx.doi.org/10.17504/protocols.io.ec9baz6 Copy
Authors: Irina Agarkova
Group: VERVE Net, The Chlorovirus Group
Proper citation: Irina Agarkova 2016. Pulse Field Gel Electrophoresis (PFGE) Protocol for separation of Chlorella chromosomal DNA and Chlorella virus DNA. protocols.io dx.doi.org/10.17504/protocols.io.essbeee Copy
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 dx.doi.org/10.17504/protocols.io.eq4bdyw Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Chlorovirus DNA Miniprep Procedure. protocols.io dx.doi.org/10.17504/protocols.io.erzbd76 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 Buffer B. protocols.io dx.doi.org/10.17504/protocols.io.esjbecn Copy
Authors: Dr. Steven Wilhelm, Samantha Coy
Group: VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/
Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Chlorella Virus Plaque Assay. protocols.io dx.doi.org/10.17504/protocols.io.hgqb3vw Copy
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. Resolving gel buffer (4X). protocols.io dx.doi.org/10.17504/protocols.io.eq3bdyn Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io dx.doi.org/10.17504/protocols.io.c34yqv Copy
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 dx.doi.org/10.17504/protocols.io.ejpbcmn Copy
Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net
Summary: For use in Viral and bacterial isolates, propagation and preparation of stocks.
Proper citation: André M. Comeau and Rachel T. Noble 2016. Pellet resuspension. protocols.io dx.doi.org/10.17504/protocols.io.dzt76m Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses
The VOCs (Virus Orthologous Clusters) database is at the heart of our system.
The database links directly to integrated tools for comparative analyses.
VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval.
Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu).
design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.
Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations
Linking to research reviews/papers for the research community.
Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases
Building new features into our tools
Help with genome annotation
Proper citation: Nick Tang 2016. VBRC Base By Base: Align entire sequences or subsequence regions. protocols.io dx.doi.org/10.17504/protocols.io.ecybaxw Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Modified after Glöckner et al. 1999
Proper citation: Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io dx.doi.org/10.17504/protocols.io.c3ayid Copy
Authors: Amy Zimmerman
Group: VERVE Net, Worden Lab
Summary: Purpose: To evaluate the influence of nutrient availability on cellular elemental composition (quotas and stoichiometry) in marine picoeukaryotes.Elemental quotas and ratios are assessed under nutrient replete and deplete conditions at the same time to minimize potential variation between experiments. Cells from an exponentially growing culture are concentrated by centrifugation, washed and re-suspended in a small volume of nutrient deplete media. These concentrated cells are used to inoculate triplicate replete and deplete culture flasks at a starting density corresponding to early-exponential growth. Culture growth is monitored daily. When the mean growth rate of the nutrient deplete treatment is half or less of the replete treatment (GRDEP/GRREP
Proper citation: Amy Zimmerman 2016. Nutrient deplete/replete algal culture for elemental analysis. protocols.io dx.doi.org/10.17504/protocols.io.fcdbis6 Copy
Authors: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder
Group: VERVE Net
Summary: The viral concentrate used for PFGE analysis must be molded into plugs, followed by lysis of the virus particles to release their DNA. It is possible to run solution-based preparation of viral DNA for PFGE (Steward 2001); however, large DNA molecules (>100 kb) are extremely sensitive to mechanical shearing in aqueous solution (Bouchez and Camilleri 1997). The consensus is that lysis inside viral plugs prevents mechanical shearing of the DNA, resulting in more discrete PFGE bands. Intact viral genomes are then separated by size by PFGE. After separation, the banding pattern is visualized by staining with a fluorescent DNA stain. This banding pattern provides a visual record of the genome size distribution that can be used for qualitative and quantitative comparisons between samples.
Proper citation: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE). protocols.io dx.doi.org/10.17504/protocols.io.dy27yd Copy
Authors: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: Long-standing questions in marine viral ecology are centered on understanding how viral assemblages change along gradients in space and time. However, investigating these fundamental ecological questions has been challenging due to incomplete representation of naturally occurring viral diversity in single gene- or morphology-based studies and an inability to identify up to 90% of reads in viral metagenomes (viromes). In this protocol, I describe how to use an annotation- and assembly-free strategy for comparative metagenomics that combines shared k-mer and social network analyses (regression modeling). This robust statistical framework enables visualization of complex sample networks and determination of ecological factors driving community structure. This tutorial describes a protocol to reproduce work from the Pacific Ocean virome comprised of 32 viromes from diverse sites in the Pacific Ocean. "Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses" (July 7, 2014, doi: 10.1073/pnas.1319778111, PNAS July 22, 2014 vol. 111 no. 29 10714-10719)Code is freely available at Github.
Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. protocols.io dx.doi.org/10.17504/protocols.io.efgbbjw Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of the trace metal mixture for addition to seawater for the cultivation of marine cyanobacteria, Prochlorococcus and Synechococcus
Proper citation: Matthew Sullivan Lab 2015. Cyanobacteria Trace Metal Mixture (CTMM). protocols.io dx.doi.org/10.17504/protocols.io.c8nzvd Copy
Authors: Chisholm Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Chisholm Lab 2016. NATURAL SEAWATER-BASED PRO99 MEDIUM. protocols.io dx.doi.org/10.17504/protocols.io.c7zzp5 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to plot contig coverage statistics, as well as sequence count and length stats. We begin with visualizing contig length vs coverage. We then visualize the distributions of sequence counts per sample as a probability density plot (similar idea as a histogram), and then do the same for median sequence length. 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 R1: Virome Contig and Sequencing Statistics. protocols.io dx.doi.org/10.17504/protocols.io.eh5bb86 Copy
Authors: Ken Stedman, Geoffrey Diemer, Jennifer E Kyle
Group: VERVE Net
Summary: An alternative epifluorescence microscopy (EFM) technique for virus enumeration has been developed using polycarbonate Track Etch (PCTE) filter membranes in place of aluminum oxide Anodisc membranes. The established EFM technique, first developed by Hennes and Suttle in 1995 and later expanded upon by Noble and Fuhrman in 1998, uses supported 20 nm pore-size Anodisc filter membranes to determine virus abundance in natural environments. Increased price and sporadic availability of Anodisc filters stimulated the evaluation of alternative filters for use in the procedure. The feasibility of using 30 nm pore-size PCTE filters for virus enumeration was assessed using the Anodisc filter procedure as a control. Although virion particle counts are slightly less precise using PCTE filters, they offer a substitute for Anodiscs while requiring only minor adjustments to the established protocol. Per slide, the PCTE costs approximately ten times less to prepare than the Anodisc-based method.
Proper citation: Ken Stedman, Geoffrey Diemer, Jennifer E Kyle 2016. PCTE Protocol for VLP enumeration. protocols.io dx.doi.org/10.17504/protocols.io.eaubaew Copy
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