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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Isolation Of Total DNA From NC64A Chlorella Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.ethbej6 | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Isolation Of Total DNA From NC64A Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.ethbej6 | 2021-04-15 09:15:13 | ||||
|
Reverse Cross-linking Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c6bzam | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Reverse Cross-linking Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6bzam | 2021-04-15 09:14:49 | ||||
|
MPN (Most Probable Number) assay for infectivity of algal viruses Resource Report Resource Website |
Amy Zimmerman | DOI:10.17504/protocols.io.gunbwve | VERVE Net, Worden Lab | Purpose: To quantify infectious viruses and evaluate the infectivity of a viral sample.50 µL of serially-diluted (10-3 to 10-10) virus sample is added to 150 µL of exponentially growing host cells in triplicate 96-well microplates and incubated at normal growth conditions for ~2 weeks. Cell lysis is assessed every few days qualitatively by visual inspection and quantitatively by measuring optical density on a microplate reader. The MPN of infective viruses in each concentrate is estimated from the proportion of virus-positive (i.e., lysed) wells using the MPN_ver4.xls Excel spreadsheet from Jarvis, B., Wilrich, C., and P.-T. Wilrich (2010), Journal of Applied Microbiology 109 (2010), 1660 – 1667. Percent infectivity is then calculated by comparing the MPN-estimated abundance of infective viruses to the abundance of virus-like particles (VLPs) determined by flow cytometry analysis. | Worden Lab, Monterey Bay Aquarium Research Institute | 3 | 2017 | Amy Zimmerman 2017. MPN (Most Probable Number) assay for infectivity of algal viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.gunbwve | 2021-04-15 09:15:24 | |||
|
Viral DNA Miniprep Procedure Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eq6bdze | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Viral DNA Miniprep Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.eq6bdze | 2021-04-15 09:14:54 | ||||
|
Train for a One-Way Mission to Mars Resource Report Resource Website |
Edmond Dion | DOI:10.17504/protocols.io.etqbemw | VERVE Net | This mock protocol is a fun description of the steps one might undertake to train for a one-way mission to the planet Mars. The One-Way mission concept is gaining popularity due to it's simpler approach and lower cost. Rather than expend effort to bring back the Marstronauts, the plan calls for leaving them there and ultimately colonizing the red planet. | 1 | 2016 | Edmond Dion 2016. Train for a One-Way Mission to Mars. protocols.io https://dx.doi.org/10.17504/protocols.io.etqbemw | 2021-04-15 09:14:53 | ||||
|
1X CviRI Assay Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.es2bege | VERVE Net | For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. 1X CviRI Assay Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.es2bege | 2021-04-15 09:15:24 | ||||
|
Positive and Negative Staining of Viruses on TEM Grids Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.day2fv | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to negatively or positively stain viruses that have been deposited onto TEM grids so that they can be imaged using transmission electron microscopy (TEM). Positive staining stains the virus itself such that the virus is dark against a lighter background (Figure 1A). This is the easiest staining to do and yields results suitable for analyzing the morphological diversity of viruses from aquatic samples. Negative staining relies on some stain remaining around the edges of a virus such that the details of the virus are clearly defined (Figure 1B). Negative staining is more difficult and is used to obtain publication quality micrographs of viruses.Note: To deposit viruses onto the grids prior to staining, use either the “Adsorbing Viruses onto TEM Grids” protocol or the “Quantitatively Depositing Viruses onto TEM Grids” protocol. Grids should be stained immediately after depositing viruses onto them. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Positive and Negative Staining of Viruses on TEM Grids. protocols.io https://dx.doi.org/10.17504/protocols.io.day2fv | 2021-04-15 09:15:19 | |||
|
CviRI Storage Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.eszbef6 | VERVE Net | For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Storage Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.eszbef6 | 2021-04-15 09:15:29 | ||||
|
Script P12: Antibiotic Resistance Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ehwbb7e | VERVE Net, Club Grice | This protocol provides a method for analysis of the relative abundance of potential antibiotic resistance genes found in the virome. We use the Comprehensive Antibiotic Resistance Database (CARD) as our reference for potential antibiotic resistance genes. | 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 | https://doi.org/10.12688/f1000research.9453.2 | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P12: Antibiotic Resistance. protocols.io https://dx.doi.org/10.17504/protocols.io.ehwbb7e | 2021-04-15 09:14:56 | |
|
Spot-on-lawn (halo) assay for screening enrichment cultures and isolates for viruses Resource Report Resource Website |
Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith | DOI:10.17504/protocols.io.eagbabw | VERVE Net | This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003).This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_057.pdf | 1 | 2015 | Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2015. Spot-on-lawn (halo) assay for screening enrichment cultures and isolates for viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.eagbabw | 2021-04-15 09:14:55 | ||
|
Analysis of Viral Morphological Characteristics Resource Report Resource Website |
Jennifer Brum | DOI:10.17504/protocols.io.dde23d | VERVE Net, Sullivan Lab | Purpose: This protocol describes how to analyze a natural aquatic virus sample using transmission electron microscopy (TEM). The purpose is to obtain the capsid diameter distributions of the viral assemblage, tail length distributions of the viral assemblage, and percentages of each viral morphotype in a sample.Note: Prior to using this protocol, deposit viruses from your sample onto a TEM grid using the protocol “Quantitatively Depositing Viruses onto TEM Grids” then stain the viruses using the protocol “Positive and Negative Staining of Viruses on TEM Grids”. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Jennifer Brum 2016. Analysis of Viral Morphological Characteristics. protocols.io https://dx.doi.org/10.17504/protocols.io.dde23d | 2021-04-15 09:15:29 | |||
|
MPN (Most Probable Number) assay for infectivity of algal viruses Resource Report Resource Website |
Amy Zimmerman | DOI:10.17504/protocols.io.fcbbisn | VERVE Net, Worden Lab | Purpose: To quantify infectious viruses and evaluate the infectivity of a viral sample.50 µL of serially-diluted (10-3 to 10-10) virus sample is added to 150 µL of exponentially growing host cells in triplicate 96-well microplates and incubated at normal growth conditions for ~2 weeks. Cell lysis is assessed every few days qualitatively by visual inspection and quantitatively by measuring optical density on a microplate reader. The MPN of infective viruses in each concentrate is estimated from the proportion of virus-positive (i.e., lysed) wells using the MPN_ver4.xls Excel spreadsheet from Jarvis, B., Wilrich, C., and P.-T. Wilrich (2010), Journal of Applied Microbiology 109 (2010), 1660 – 1667. Percent infectivity is then calculated by comparing the MPN-estimated abundance of infective viruses to the abundance of virus-like particles (VLPs) determined by flow cytometry analysis. | Monterey Bay Aquarium Research Institute | 1 | 2016 | Amy Zimmerman 2016. MPN (Most Probable Number) assay for infectivity of algal viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.fcbbisn | 2021-04-15 09:15:31 | |||
|
Bacteriophage isolation by spotting on target host cells Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dps5nd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Phage lysis of host bacteria can be visualized by plaque formation on lawns of host cells in soft agar overlayed on agar plates (Adams, 1959; Sambrook et al. 1989). This principle can be used for the detection and subsequent isolation of specific lytic phages in environmental samples (e.g., Carlson 2005). Spotting environmental samples on lawns of a target host cell would thus reveal the presence of a lytic phage for that particular host cell in the given sample. | 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. Bacteriophage isolation by spotting on target host cells. protocols.io https://dx.doi.org/10.17504/protocols.io.dps5nd | 2021-04-15 09:15:02 | ||
|
Isolation and Purification of DNA from Chlorella Viruses Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eq5bdy6 | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Isolation and Purification of DNA from Chlorella Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.eq5bdy6 | 2021-04-15 09:15:00 | ||||
|
TFB buffer Resource Report Resource Website |
James Thornton | DOI:10.17504/protocols.io.eq9bdz6 | VERVE Net | Hurwitz Lab | 1 | 2016 | James Thornton 2016. TFB buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.eq9bdz6 | 2021-04-15 09:15:33 | ||||
|
Extracting nucleic acids from viruses on a filter Resource Report Resource Website |
Grieg F. Steward and Alexander I. Culley | DOI:10.17504/protocols.io.dsm6c5 | VERVE Net | This protocol is a minor modification of that reported by Culley and Steward (2007). As the starting point for this protocol, we assume that viruses have been collected on an aluminum oxide 0.02-µm syringe-tip filter (Anotop, Whatman), but other filters capable of capturing viruses may be substituted.This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_154.pdf | 1 | 2015 | Grieg F. Steward and Alexander I. Culley 2015. Extracting nucleic acids from viruses on a filter. protocols.io https://dx.doi.org/10.17504/protocols.io.dsm6c5 | 2021-04-15 09:15:09 | ||
|
Propagation of marine eukaryotic viruses (Prasinoviruses) Resource Report Resource Website |
Amy Zimmerman | DOI:10.17504/protocols.io.gujbwun | VERVE Net, Worden Lab | Purpose: To reproducibly generate fresh preparations of virus for independent experiments.Fresh virus sample for an experiment is generated by a primary infection of exponentially growing host cells from a master stock of virus. The infected host is allowed to lyse until the culture is cleared. The lysate is filtered to remove any large cellular debris, then the viral-size fraction is concentrated from the filtered lysate and washed with buffer using a centrifugal concentrator. The viral concentrate is stored at 4°C protected from light and should be used for an experiment within 1-2 days. On the day of (or the day before) the experiment, an MPN assay should be set up to assess infectivity of the fresh viral concentrate. | Worden Lab, Monterey Bay Aquarium Research Institute | 2 | 2017 | Amy Zimmerman 2017. Propagation of marine eukaryotic viruses (Prasinoviruses). protocols.io https://dx.doi.org/10.17504/protocols.io.gujbwun | 2021-04-15 09:15:13 | |||
|
GraPhlAn visualization of single and multiple samples Resource Report Resource Website |
Curtis Huttenhower | DOI:10.17504/protocols.io.d9s96d | VERVE Net, Huttenhower Lab | In this protocol we describe some approaches to graphically represent single profiled samples or a merged table of relative abundances. | https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial | 1 | 2016 | Curtis Huttenhower 2016. GraPhlAn visualization of single and multiple samples. protocols.io https://dx.doi.org/10.17504/protocols.io.d9s96d | 2021-04-15 09:15:36 | |||
|
Nutrient deplete/replete algal culture for elemental analysis Resource Report Resource Website |
Amy Zimmerman, Susanne Wilken | DOI:10.17504/protocols.io.gukbwuw | VERVE Net, Worden Lab | 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 | Worden Lab, Monterey Bay Aquarium Research Institute, Worden Lab, Monterey Bay Aquarium Research Institute | 2 | 2017 | Amy Zimmerman, Susanne Wilken 2017. Nutrient deplete/replete algal culture for elemental analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.gukbwuw | 2021-04-15 09:15:11 | |||
|
Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging Resource Report Resource Website |
Li Deng, Bonnie T. Poulos, Matthew B. Sullivan | DOI:10.17504/protocols.io.c6zzf5 | VERVE Net, Sullivan Lab | AbstractOcean viruses are abundant, ubiquitous, and play important roles in global biogeochemical cycles through mortality, horizontal gene transfer and manipulation of host metabolism. However, the ability to link viruses to their hosts in a high-throughput manner bottlenecks our ability to understand virus-host interactions in complex communities. Here, we present viral tagging (VT), a method that combines mixtures of isotope labeled host cells and fluorescent viruses with flow cytometry. In a single experiment, we can screen 107 uncultivated ocean viruses with a single strain of Synechococcus. These viruses can then be sequenced to quantitatively link objectivelydefined environmental viral populations, and their genomes, to their hosts. | 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 | Li Deng, Bonnie T. Poulos, Matthew B. Sullivan 2016. Obtaining targeted metagenomes from uncultivated environmental Synechococcus using flow cytometry-based viral tagging. protocols.io https://dx.doi.org/10.17504/protocols.io.c6zzf5 | 2021-04-15 09:15:38 |
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
