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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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phageFISH Protocol Resource Report Resource Website |
Cristina Moraru & Elke Allers | DOI:10.17504/protocols.io.c9iz4d | VERVE Net, Sullivan Lab | This protocol combines phage gene detection with rRNA detection for the identification of host cells and detection of free phage particles. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Cristina Moraru & Elke Allers 2016. phageFISH Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c9iz4d | 2021-04-15 09:15:57 | |||
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Quality Control of Reads Using Trimmomatic (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.gvybw7w | VERVE Net, Sullivan Lab, iVirus | A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.Quality trimming of reads is important! | The Ohio State University | 1 | 2016 | Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.gvybw7w | 2021-04-15 09:15:58 | |||
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How to make your protocol more reproducible, discoverable, and user-friendly Resource Report Resource Website |
protocols.io team | DOI:10.17504/protocols.io.g7vbzn6 | VERVE Net, protocols.io news, Protist Research to Optimize Tools in Genetics (PROT-G) | Protocols.io offers extensive flexibility in entering and presenting detailed methods. However, simple suggestions in here can help to make your protocol more useful to you and others. Importantly, easy steps outlined here can greatly increase the visibility of your protocol and ensure that scientists who need can find it.If you have any questions, please feel free to reach out to the protocols.io team by e-mailing us at info [at] protocols.io. | protocols.io | 1 | 2019 | protocols.io team 2019. How to make your protocol more reproducible, discoverable, and user-friendly. protocols.io https://dx.doi.org/10.17504/protocols.io.g7vbzn6 | 2021-04-15 09:15:55 | |||
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Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.c54y8v | VERVE Net, Sullivan Lab | This protocol describes how to concentrate viruses in liquid samples using an Amicon or Nanosep centrifugal ultrafiltration device. We use Amicons to concentrate medium volumes of samples (10s to 100s of mls) down to a final volume of ~4 ml. We use Nanoseps to concentrate smaller volumes of sample ( | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Concentrating Viruses with an Amicon or Nanosep Centrifugal Ultrafiltration Device. protocols.io https://dx.doi.org/10.17504/protocols.io.c54y8v | 2021-04-15 09:16:02 | |||
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Making a hit science video Resource Report Resource Website |
Lenny Teytelman | DOI:10.17504/protocols.io.emqbc5w | VERVE Net | This is a highly reproducible method for creating hit science videos. Guaranteed to lead to millions of views, fame, faculty position, tenure, and stable funding.* Legal disclaimer: This is not a peer reviewed protocol. Therefore, all claims should be taken with as much skepticism as anything that is peer reviewed. | protocols.io | 1 | 2016 | Lenny Teytelman 2016. Making a hit science video. protocols.io https://dx.doi.org/10.17504/protocols.io.emqbc5w | 2021-04-15 09:16:00 | |||
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Lysis Buffer (20 mL) Resource Report Resource Website |
Matt Sullivan Lab | DOI:10.17504/protocols.io.c4gytv | VERVE Net, Sullivan Lab | Must be made fresh before experiment because of the Sucrose. For 20 mL solutions. | Matt Sullivan Lab | 1 | 2017 | Matt Sullivan Lab 2017. Lysis Buffer (20 mL). protocols.io https://dx.doi.org/10.17504/protocols.io.c4gytv | 2021-04-15 09:16:04 | |||
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Formulation of MBBM (Modified Bold's Basal Medium) Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.etwbepe | VERVE Net | This medium is for growing Chlorella variabilis NC64A, Chlorella heliozoae SAG 3.83, and Coccomyxa C-169. | University of Nebraska | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Formulation of MBBM (Modified Bold's Basal Medium). protocols.io https://dx.doi.org/10.17504/protocols.io.etwbepe | 2021-04-15 09:15:58 | |||
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MetaPhlAn output merge and visualization Resource Report Resource Website |
Curtis Huttenhower | DOI:10.17504/protocols.io.d9q95v | VERVE Net, Huttenhower Lab | In this protocol, we will merge the 20 profiled metagenomes in a table of relative abundances and visualize the table with a heatmap. | https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial | 1 | 2016 | Curtis Huttenhower 2016. MetaPhlAn output merge and visualization. protocols.io https://dx.doi.org/10.17504/protocols.io.d9q95v | 2021-04-15 09:15:58 | |||
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K-mer-based host screening Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | DOI:10.17504/protocols.io.ehjbb4n | VERVE Net, Hurwitz Lab | K-mer-based approaches to determining sequence similiarity can be faster than traditional use of BLAST. This application uses Jellyfish to index host FASTA files, then uses the mode value (default 2) of the number of matching k-mers (default k=20) from the input sequence to determine whether the sequence is similar enough to the host sequence to be rejected. The output of the app is:"screened" directory containing the sequences from each file that were found to be dissimlar to the host"rejected" directory containing the sequence from each file that were too similar to the host"jf" directory containing Jellyfish indexes of each "host" file (useful for later runs with other files to skip recreating)"kmer" directory containing k-mers of query sequences and ".loc" file showing the number of ".kmer" lines associated to each sequence Code is freely available at Github. | University of Arizona, University of Arizona | 1 | 2016 | Bonnie Hurwitz, Ken Youens-Clark 2016. K-mer-based host screening. protocols.io https://dx.doi.org/10.17504/protocols.io.ehjbb4n | 2021-04-15 09:16:06 | |||
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Generation of DNA fragments by DNase digestion Resource Report Resource Website |
William H. Wilson and Declan Schroeder | DOI:10.17504/protocols.io.dy47yv | VERVE Net | Generation of DNA fragments by DNase digestion involves digesting DNA for a range of times, then picking the time that gives optimal-sized DNA fragments (typically 1000–4000 bp). | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_134.pdf | 1 | 2016 | William H. Wilson and Declan Schroeder 2016. Generation of DNA fragments by DNase digestion. protocols.io https://dx.doi.org/10.17504/protocols.io.dy47yv | 2021-04-15 09:16:01 | ||
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Pulse Field Gel Electrophoresis (PFGE) Protocol for separation of Chlorella chromosomal DNA and Chlorella virus DNA Resource Report Resource Website |
Irina Agarkova | DOI:10.17504/protocols.io.essbeee | VERVE Net, The Chlorovirus Group | University of Nebraska-Lincoln | 1 | 2016 | Irina Agarkova 2016. Pulse Field Gel Electrophoresis (PFGE) Protocol for separation of Chlorella chromosomal DNA and Chlorella virus DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.essbeee | 2021-04-15 09:16:03 | ||||
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Running PCPipe (protein clustering) in iPlant Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | DOI:10.17504/protocols.io.ef8bbrw | VERVE Net, Hurwitz Lab | Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology." PLoS One 8.2 (2013): e57355. | University of Arizona, University of Arizona | 1 | 2016 | Bonnie Hurwitz, Ken Youens-Clark 2016. Running PCPipe (protein clustering) in iPlant. protocols.io https://dx.doi.org/10.17504/protocols.io.ef8bbrw | 2021-04-15 09:16:05 | |||
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Isolation of cyanophages by plaque assays Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqg5tv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | More than 40 years ago, Safferman and Morris (1963) used the plaque assay method to isolate the first cyanophage that infects a freshwater filamentous cyanobacterium, Plectonema boryanum. Since then, this approach has been used successfully to detect and isolate a number of different phages infecting marine Synechoccocus and Prochlorococcus (e.g., Suttle and Chan 1993; Waterbury and Valois 1993; Wilson et al. 1993; Sullivan et al. 2003).The advantages of this method are that results are easily interpreted as plaques formed on pigmented lawns can be easily identified. Since a plaque is the result of a single infection event, the virus can be easily purified and cloned. The first part of the procedures described as follows: (1) preparation of base plates and (2) preparation of top agar/agarose are applicable also for bacteriophage plaque assays. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Isolation of cyanophages by plaque assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dqg5tv | 2021-04-15 09:16:07 | ||
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Can Crusher-Culley Protocol Resource Report Resource Website |
Alexander Culley, Grieg Steward | DOI:10.17504/protocols.io.c3jykm | VERVE Net, Sullivan Lab | Culley Protocol (from Culley & Steward (2007), New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences, Applied & Environmental Microbiology 73(18):5937-5944). | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Alexander Culley, Grieg Steward 2015. Can Crusher-Culley Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c3jykm | 2021-04-15 09:16:08 | |||
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SYBR Gold Staining for Viral Enumeration (Case 1) Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c69zh5 | VERVE Net, Sullivan Lab | Case 1: Quick check of viral concentration. Use this protocol when you can count your samples in a few days.For when long term storage of slide is required, see Case 2. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 1). protocols.io https://dx.doi.org/10.17504/protocols.io.c69zh5 | 2021-04-15 09:16:08 | |||
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Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE) Resource Report Resource Website |
Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder | DOI:10.17504/protocols.io.dy27yd | VERVE Net | 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. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_009.pdf | 1 | 2016 | Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE). protocols.io https://dx.doi.org/10.17504/protocols.io.dy27yd | 2021-04-15 09:16:06 | ||
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Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses Resource Report Resource Website |
Bonnie Hurwitz, Ken Youens-Clark | DOI:10.17504/protocols.io.efgbbjw | VERVE Net, Hurwitz Lab | 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. | University of Arizona, University of Arizona | http://www.pnas.org/content/111/29/10714.full | 1 | 2016 | Bonnie Hurwitz, Ken Youens-Clark 2016. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. protocols.io https://dx.doi.org/10.17504/protocols.io.efgbbjw | 2021-04-15 09:16:07 | ||
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Treatments and Preservation of Seawater Samples for FISH Resource Report Resource Website |
Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer | DOI:10.17504/protocols.io.c5by2m | VERVE Net, Sullivan Lab | This protocol gives a method for treatment and preservation of seawater samples that will be subject to fluorescence in situ hybridization (FISH). Samples are used with fluorescent probes to determine what populations of bacteria or other microbes are present. The filters may also be used to simply count the number of microbes in a sample. Requires varying amounts of 10µm or 200µm filtrate (up to 11.5L for open ocean depth profile) as shown in Table I. | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Bonnie Poulos, Jenn Brum, Elke Allers, Christine Schirmer 2015. Treatments and Preservation of Seawater Samples for FISH. protocols.io https://dx.doi.org/10.17504/protocols.io.c5by2m | 2021-04-15 09:16:11 | |||
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Script R1: Virome Contig and Sequencing Statistics Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.eh5bb86 | VERVE Net, Club Grice | 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. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R1: Virome Contig and Sequencing Statistics. protocols.io https://dx.doi.org/10.17504/protocols.io.eh5bb86 | 2021-04-15 09:16:11 | |
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NATURAL SEAWATER-BASED PRO99 MEDIUM Resource Report Resource Website |
Chisholm Lab | DOI:10.17504/protocols.io.c7zzp5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Chisholm Lab 2016. NATURAL SEAWATER-BASED PRO99 MEDIUM. protocols.io https://dx.doi.org/10.17504/protocols.io.c7zzp5 | 2021-04-15 09:16:10 |
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