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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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SYBR Gold Staining for viral enumeration using 13 mm Anodisc 0.02 ?m filters Resource Report Resource Website |
Li Deng & Jennifer Brum | DOI:10.17504/protocols.io.c7cziv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | 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 | 2021-04-15 09:15:49 | ||||
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Estimation of viral-induced phytoplankton mortality using the modified dilution method Resource Report Resource Website |
Susan A. Kimmance and Corina P. D. Brussaard | DOI:10.17504/protocols.io.dpf5jm | VERVE Net | 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. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_065.pdf | 1 | 2016 | 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 | 2021-04-15 09:15:28 | ||
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Script R9: Plotting Microbial Taxonomy from MEGAN Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejdbci6 | VERVE Net, Club Grice | 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. | 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 R9: Plotting Microbial Taxonomy from MEGAN. protocols.io https://dx.doi.org/10.17504/protocols.io.ejdbci6 | 2021-04-15 09:15:28 | |
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Large Volume Marine Cyanophage Phage Purification Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3iykd | VERVE Net, Sullivan Lab | Last optimized January 2006, updated by Matt on March 16 2009 | Matthew Sullivan | 1 | 2016 | Matthew Sullivan 2016. Large Volume Marine Cyanophage Phage Purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3iykd | 2021-04-15 09:15:49 | |||
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Script P1: Pre-Processing Samples Resource Report Resource Website |
Hannigan GD, Grice EA, et al. | DOI:10.17504/protocols.io.edrba56 | VERVE Net, Club Grice | 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. | 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 | Grice Lab, Department of Dermatology University of Pennsylvania, Grice Lab, Department of Dermatology University of Pennsylvania, Grice Lab, 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 P1: Pre-Processing Samples. protocols.io https://dx.doi.org/10.17504/protocols.io.edrba56 | 2021-04-15 09:15:25 | |
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FISH Protocol for FISH & FLOW Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dfe3jd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. FISH Protocol for FISH & FLOW. protocols.io https://dx.doi.org/10.17504/protocols.io.dfe3jd | 2021-04-15 09:15:30 | ||||
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Cesium Chloride Gradients Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c7dzi5 | VERVE Net, Sullivan Lab | 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). | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Cesium Chloride Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.c7dzi5 | 2021-04-15 09:15:30 | |||
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Use Bambus2 scaffolding module Resource Report Resource Website |
Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. | DOI:10.17504/protocols.io.d7n9md | VERVE Net, Hurwitz Lab | 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. | Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab, Sakakibara Lab | http://metavelvet.dna.bio.keio.ac.jp/MV.html | 1 | 2016 | 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 | 2021-04-15 09:15:33 | ||
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QIIME:Moving Pictures of the human microbiome Resource Report Resource Website |
Bonnie Hurwitz | DOI:10.17504/protocols.io.d5288d | VERVE Net, Hurwitz Lab, ABE487_HMP, ABE487_EMP | 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. | 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 | University of Arizona | http://nbviewer.ipython.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb | 1 | 2015 | Bonnie Hurwitz 2015. QIIME:Moving Pictures of the human microbiome. protocols.io https://dx.doi.org/10.17504/protocols.io.d5288d | 2021-04-15 09:15:52 | |
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Unix and Bioinformatics Resource Report Resource Website |
Benjamin Tully | DOI:10.17504/protocols.io.eptbdnn | VERVE Net, ECOGEO | This protocol details the use of various unix commands commonly used in bioinformatics. | EARTHCUBE OCEANOGRAPHY AND GEOBIOLOGY ENVIRONMENTAL 'OMICS | 1 | 2016 | Benjamin Tully 2016. Unix and Bioinformatics. protocols.io https://dx.doi.org/10.17504/protocols.io.eptbdnn | 2021-04-15 09:15:37 | |||
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Centrifuged Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddj24m | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddj24m | 2021-04-15 09:15:35 | |||
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Low input Library Preparation for Illumina Sequencing Resource Report Resource Website |
Adriana Alberti | DOI:10.17504/protocols.io.ddq25v | VERVE Net, Sullivan Lab | 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. | Teytelman L, Stoliartchouk A, Kindler L, Hurwitz BL, Protocols.io: Virtual Communities for Protocol Development and Discussion. PLoS Biology 14(8). doi: 10.1371/journal.pbio.1002538 | Matthew Sullivan Lab | https://doi.org/10.1371/journal.pbio.1002538 | 1 | 2016 | Adriana Alberti 2016. Low input Library Preparation for Illumina Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.ddq25v | 2021-04-15 09:15:35 | |
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Host Range Protocols Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dew3fd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Host Range Protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.dew3fd | 2021-04-15 09:15:36 | ||||
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Stacking gel buffer (4X) Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.eq4bdyw | VERVE Net | For use in Polyacrylamide Gel System For Electrophoresis Of Proteins. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. Stacking gel buffer (4X). protocols.io https://dx.doi.org/10.17504/protocols.io.eq4bdyw | 2021-04-15 09:15:40 | ||||
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FLV tracer assays Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | DOI:10.17504/protocols.io.dzu76v | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_019.pdf | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. FLV tracer assays. protocols.io https://dx.doi.org/10.17504/protocols.io.dzu76v | 2021-04-15 09:15:43 | |||
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Virus and bacteria counts by epifluorescence microscopy with SYBR Green Resource Report Resource Website |
Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, Jed A Fuhrman | DOI:10.17504/protocols.io.r2dd8a6 | VERVE Net, Fuhrman Lab | 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. | Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab, Fuhrman Lab | http://www.nature.com/nprot/journal/v2/n2/full/nprot.2007.6.html | 2 | 2018 | 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 | 2021-04-15 09:15:40 | ||
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Working Bead Solution Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c84zyv | VERVE Net, Sullivan Lab | For use in Wet-mount Method for Enumeration of Aquatic Viruses | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Working Bead Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c84zyv | 2021-04-15 09:15:39 | |||
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Chlorovirus DNA Miniprep Procedure Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.erzbd76 | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Chlorovirus DNA Miniprep Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.erzbd76 | 2021-04-15 09:15:41 | ||||
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TE Buffer Resource Report Resource Website |
Ms Alex Aitken | DOI:10.17504/protocols.io.c5uy6v | VERVE Net, Sullivan Lab | 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 | http://www.nhm.ac.uk/resources-rx/files/te-buffer_aug12-118648.pdf | 1 | 2016 | Ms Alex Aitken 2016. TE Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.c5uy6v | 2021-04-15 09:15:46 | |||
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Script R15: CoNet Analysis - Formatting Relative Abundance Files Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejpbcmn | VERVE Net, Club Grice | 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. | 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 R15: CoNet Analysis - Formatting Relative Abundance Files. protocols.io https://dx.doi.org/10.17504/protocols.io.ejpbcmn | 2021-04-15 09:15:57 |
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