Protocols   Select Another Resource Report Type

Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stocks (liquid assay)"

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Clonal virus purification. protocols.io https://dx.doi.org/10.17504/protocols.io.dqp5vm Copy   

•   Source:

Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: Protocol for labeling bacteria with N15. The bacterial DNA was made “heavy” so that community viral and host bacterial DNA could be distinguished from each other after sorting by using density gradient centrifugation.

Proper citation: Bonnie Poulos 2016. Isotopic Labeling of Cyanobacteria and DNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.c9nz5d Copy   

•   Source:

Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly infected cells (FVIC), the frequency of infected cells (FIC), the fraction of mortality due to viral lysis (FMVL), and burst size.

Proper citation: Jennifer Brum 2016. FVIC (Frequency of Visibly Infected Cells) Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dbp2mm Copy   

•   Source:

Authors: Ms Alex Aitken
Group: VERVE Net, Sullivan Lab
Summary: This shows how to make 0.5M EDTA

Proper citation: Ms Alex Aitken 2016. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c5wy7d Copy   

•   Source:

Authors: Steven M. Short, Feng Chen, and Steven W. Wilhelm
Group: VERVE Net
Summary: Marker genes for viruses are typically amplified from aquatic samples to determine whether specific viruses are present in the sample, or to examine the diversity of a group of related viruses. In this [protocol], we will provide an overview of common methods used to amplify, clone, sequence, and analyze virus marker genes, and will focus our discussion on viruses infecting algae, bacteria, and heterotrophic flagellates.Short, S. M., F. Chen, and S. W. Wilhelm. 2010. The construction and analysis of marker gene libraries, p. 82–91. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.

Proper citation: Steven M. Short, Feng Chen, and Steven W. Wilhelm 2015. The construction and analysis of marker gene libraries. protocols.io https://dx.doi.org/10.17504/protocols.io.dpi5kd Copy   

•   Source:

Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Gradient Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.eufbetn Copy   

•   Source:

Authors: David Dunigan and Irina Agarkova
Group: VERVE Net, Fish behavior and physiology, Medicinal Plants Southeastern Pará Research Group

Proper citation: David Dunigan and Irina Agarkova 2016. Lowry Protein Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.etxbepn Copy   

•   Source:

Authors: Qiagen
Group: VERVE Net, Sullivan Lab
Summary: This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A

Proper citation: Qiagen 2017. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.hxgb7jw Copy   

•   Source:

Authors: Rebecca Heald Lab
Group: VERVE Net
Summary: This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.

Proper citation: Rebecca Heald Lab 2015. Heald Lab Margaritas. protocols.io https://dx.doi.org/10.17504/protocols.io.ea8bahw Copy   

•   Source:

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: Export a sequence selection to a different file. protocols.io https://dx.doi.org/10.17504/protocols.io.eckbauw Copy   

•   Source:

Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Obtaining pure cyanophage stocks (plaque purification). protocols.io https://dx.doi.org/10.17504/protocols.io.dqq5vv Copy   

•   Source:

Authors: Numerous scientists
Group: VERVE Net
Summary: This collection is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.If you know creative/unusual protocols like these, please tweet them to #ExoticMethods, e-mail to "[email protected]", or share directly as a protocol here, tagging with "ExoticMethods".

Proper citation: Numerous scientists 2016. Exotic Lab Methods. protocols.io https://dx.doi.org/10.17504/protocols.io.ebhbaj6 Copy   

•   Source:

Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab

Proper citation: Natalie Solonenko 2016. 16S PCR Universal. protocols.io https://dx.doi.org/10.17504/protocols.io.c5my45 Copy   

•   Source:

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: View gene annotations. protocols.io https://dx.doi.org/10.17504/protocols.io.ecqbavw Copy   

•   Source:

Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. One-Step Growth Curves for Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.dan2dd Copy   

•   Source:

Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Isolation and Purification of Plasmid DNA from E. coli. protocols.io https://dx.doi.org/10.17504/protocols.io.ertbd6n Copy   

•   Source:

Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.

Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. protocols.io https://dx.doi.org/10.17504/protocols.io.d7q9mv Copy   

•   Source:

Authors: Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: See upcoming paper by Watts, Hurwitz, Youens-Clark.Code is freely available at Github.

Proper citation: Ken Youens-Clark 2016. Running "16sblaster" at iPlant. protocols.io https://dx.doi.org/10.17504/protocols.io.egmbbu6 Copy   

•   Source:

Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used for intra and interpersonal diversity of the virome and whole metagenome using the Bray Curtis dissimilarity metric. We visualize the differences as bar plots and calculate the statistical significance of the differences using a t-test. 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 R7: Intra and Inter Personal Dissimilarity. protocols.io https://dx.doi.org/10.17504/protocols.io.eipbcdn Copy   

•   Source:

Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Preparation of PBCV-1 Lysin. protocols.io https://dx.doi.org/10.17504/protocols.io.etdbei6 Copy   

•   Source: