Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Adsorbing Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | 10.17504/protocols.io.dar2d5 | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with high concentrations of viruses. For natural samples, use the protocol “Quantitatively Depositing Viruses onto TEM Grids using an Airfuge”.Note: If purification of the viruses is necessary, refer to Ackermann and Heldal (2010) for various options. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Adsorbing Viruses on TEM Grids. protocols.io dx.doi.org/10.17504/protocols.io.dar2d5 | 2021-03-29 03:10:39 | |||
|
Transcriptomics During One-Step Growth Curves for Cellulophaga Phages Resource Report Resource Website |
Bonnie Poulos | 10.17504/protocols.io.ek4bcyw | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.ek4bcyw | 2021-03-29 03:10:34 | ||||
|
SYBR Gold Staining for Viral Enumeration (Case 2) Resource Report Resource Website |
Li Deng | 10.17504/protocols.io.c7fzjm | VERVE Net, Sullivan Lab | Case 2: Fix samples. Use this protocol when long term storage of slide is required.For when you can count your samples in a few days, see Case 1. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 2). protocols.io dx.doi.org/10.17504/protocols.io.c7fzjm | 2021-03-29 03:10:35 | |||
|
Top agarose Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | 10.17504/protocols.io.dqh5t5 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | For use in "Isolation of cyanophages by plaque assyays" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Top agarose. protocols.io dx.doi.org/10.17504/protocols.io.dqh5t5 | 2021-03-29 03:10:44 | |||
|
Script R5: Virome Alpha Diversity Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | 10.17504/protocols.io.eimbcc6 | VERVE Net, Club Grice | This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. 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 R5: Virome Alpha Diversity. protocols.io dx.doi.org/10.17504/protocols.io.eimbcc6 | 2021-03-29 03:10:42 | |
|
VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search) Resource Report Resource Website |
Nick Tang | 10.17504/protocols.io.eczbax6 | VERVE Net, Upton-Lab | 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 | University of Victoria: Department of Biochemistry and Microbiology | http://athena.bioc.uvic.ca/ | 1 | 2016 | Nick Tang 2016. VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search). protocols.io dx.doi.org/10.17504/protocols.io.eczbax6 | 2021-03-29 03:10:45 | ||
|
CviJI Buffer A Resource Report Resource Website |
David Dunigan and Irina Agarkova | 10.17504/protocols.io.esibece | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | David Dunigan and Irina Agarkova 2016. CviJI Buffer A. protocols.io dx.doi.org/10.17504/protocols.io.esibece | 2021-03-29 03:10:51 | ||||
|
Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.dep3dm | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.dep3dm | 2021-03-29 03:10:51 | |||
|
Titration of AmPure XP Beads for Removal of Fragments Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.c52y8d | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Titration of AmPure XP Beads for Removal of Fragments . protocols.io dx.doi.org/10.17504/protocols.io.c52y8d | 2021-03-29 03:10:45 | ||||
|
Cellulophaga growth reading Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.dpa5id | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io dx.doi.org/10.17504/protocols.io.dpa5id | 2021-03-29 03:10:55 | |||
|
10g/L Fe Stock Solution Resource Report Resource Website |
Matthew Sullivan Lab | 10.17504/protocols.io.c2zyf5 | VERVE Net, Sullivan Lab | 10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 10g/L Fe Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.c2zyf5 | 2021-03-29 03:11:04 | |||
|
Concentration of viruses and preparation of FLVs for tracer assays Resource Report Resource Website |
André M. Comeau and Rachel T. Noble | 10.17504/protocols.io.dzv765 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | The steps describe how to prepare each virus concentrate. There are multiple options for many of the steps; in the case where there is more than one option they are noted in annotations. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_019.pdf | 1 | 2016 | André M. Comeau and Rachel T. Noble 2016. Concentration of viruses and preparation of FLVs for tracer assays. protocols.io dx.doi.org/10.17504/protocols.io.dzv765 | 2021-03-29 03:09:31 | ||
|
RNAlater Recipe Resource Report Resource Website |
Rex Malmstrom | 10.17504/protocols.io.c56y9d | VERVE Net, Sullivan Lab | This is a storage solution that stabilizes and protectsRNA while inactivating RNase | MIT/Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Rex Malmstrom 2015. RNAlater Recipe. protocols.io dx.doi.org/10.17504/protocols.io.c56y9d | 2021-03-29 03:09:29 | |||
|
BiMat: a MATLAB package to facilitate the analysis of bipartite networks Resource Report Resource Website |
Joshua Weitz | 10.17504/protocols.io.fajbicn | VERVE Net | BiMat: a MATLAB package to facilitate the analysis of bipartite networks. Extensive documentation, code, and worked examples available on: http://bimat.github.ioThe datasets included with the package include phage-bacterai infection networks. | Georgia Institute of Technology | http://bimat.github.io | 1 | 2016 | Joshua Weitz 2016. BiMat: a MATLAB package to facilitate the analysis of bipartite networks. protocols.io dx.doi.org/10.17504/protocols.io.fajbicn | 2021-03-29 03:09:30 | ||
|
Dot Blot Preparation Resource Report Resource Website |
David Dunigan and Irina Agarkova | 10.17504/protocols.io.etibeke | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Dot Blot Preparation. protocols.io dx.doi.org/10.17504/protocols.io.etibeke | 2021-03-29 03:09:34 | ||||
|
Detecting Fungal Infections in Almonds Resource Report Resource Website |
Carolina Cadena | 10.17504/protocols.io.etnbeme | VERVE Net | This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format. Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72 | 1 | 2016 | Carolina Cadena 2016. Detecting Fungal Infections in Almonds. protocols.io dx.doi.org/10.17504/protocols.io.etnbeme | 2021-03-29 03:09:35 | ||||
|
CsCl Step Gradient Buffer Resource Report Resource Website |
Jonathan King | 10.17504/protocols.io.dmj44m | VERVE Net, Sullivan Lab | This mixture is used in the CsCl Step Gradient to Purify Phage Protocol | King Lab, MIT | http://web.mit.edu/king-lab/www/cookbook/cscl_grad_phage.htm | 1 | 2016 | Jonathan King 2016. CsCl Step Gradient Buffer. protocols.io dx.doi.org/10.17504/protocols.io.dmj44m | 2021-03-29 03:09:36 | ||
|
Applying vContact to Viral Sequences and Visualizing the Output (Cyverse) Resource Report Resource Website |
Benjamin Bolduc | 10.17504/protocols.io.x5xfq7n | 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. | The Ohio State University | https://doi.org/10.1101/533240 | 5 | 2019 | Benjamin Bolduc 2019. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.x5xfq7n | 2021-03-29 03:09:41 | ||
|
Wet-mount Method for Enumeration of Aquatic Viruses Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | 10.17504/protocols.io.c8pzvm | VERVE Net, Sullivan Lab | Purpose: This method for the enumeration of aquatic viruses is a low-cost alternative to the commonly used filter-mount method. Briefly, fluorescently-stained samples are wetmounted directly onto slides for epifluorescence microscopy after an optional chemical flocculation concentration step used for samples with anticipated virus concentrations of 7 viruses mL-1 (samples with >5×107 viruses mL-1 do not require this concentration step prior to analysis). Virus concentration in the wet-mounted sample is determined from the ratio of viruses to microsphere beads, which are added at a known concentration. This wet-mount method for enumerating viruses is significantly less expensive than the filter-mount method (i.e., the cost of microsphere beads per sample is ~500-fold lower than the cost of one filter per sample), and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations encountered in field and laboratory samples. The only limitation of this method is that samples with virus concentrations ≤1×106 viruses mL-1 cannot be enumerated, as the abundance of viruses is too low for efficient enumeration.Figure 1. Overview of the wet-mount method for enumeration of aquatic viruses. | 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, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Wet-mount Method for Enumeration of Aquatic Viruses. protocols.io dx.doi.org/10.17504/protocols.io.c8pzvm | 2021-03-29 03:09:37 | |||
|
0.5M NH4Cl Resource Report Resource Website |
Matthew Sullivan Lab | 10.17504/protocols.io.c77zrm | VERVE Net, Sullivan Lab | Supplement to seawater for growth of cyanobacteria. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm | 2021-03-29 03:09:44 |
Can't find your Protocol?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. If you want to find a specific protocol and you know the DOI of the protocol already, it's easier to enter a DOI to search. You can refine the search results using Facets on the left side of the search results page. If you are on the table view, you can also search in a specific column by clicking the column title and enter the keywords.
If you still could not find your protocol in the search results, please help us by adding it into the system — it's easy. Create and publish your protocols at Protocols.io.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
