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 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PSS2 PCR Protocol Resource Report Resource Website |
Mel Duhaime | DOI:10.17504/protocols.io.dfm3k5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Mel Duhaime 2016. PSS2 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfm3k5 | 2021-04-15 09:14:22 | ||||
|
EDTA disodium salt dihydrate Resource Report Resource Website |
James Thornton | DOI:10.17504/protocols.io.dbm2k5 | VERVE Net, Sullivan Lab | For use in DNase I Treatment protocol for DNase inactivation. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 | 2021-04-15 09:14:34 | |||
|
Coring Technique Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c3zyp5 | VERVE Net, Sullivan Lab | This is a technique for isolating phage from agar plates. When working with lytic phage, well-isolated, cleared areas in a lawn of bacteria (called plaques) are removed from the agar (by coring with a sterile pipette) and used to infect fresh bacteria in liquid medium. The lysed culture can be used for a new plaque assay after 0.2 um filtering to remove residual bacteria. New phage are "plaque-purified" a minimum of three times before they are considered to be free of other phage. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. Coring Technique. protocols.io https://dx.doi.org/10.17504/protocols.io.c3zyp5 | 2021-04-15 09:14:31 | |||
|
One-step growth curves for Cellulophaga phages Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddh235 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddh235 | 2021-04-15 09:14:27 | ||||
|
Zobell Agar/Broth Medium Resource Report Resource Website |
Shalaja Srinagesh et al | DOI:10.17504/protocols.io.dbn2md | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbn2md | 2021-04-15 09:14:33 | ||||
|
Soil viral extraction protocol for ssDNA & dsDNA viruses Resource Report Resource Website |
Gary Trubl, Natalie Solonenko | DOI:10.17504/protocols.io.hu3b6yn | Sullivan Lab | Resuspend viruses from soils and sediments | OSU, OSU | 1 | 2017 | Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.hu3b6yn | 2021-04-15 09:14:39 | |||
|
Double SPRI for Second Generation Sequencing Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c53y8m | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c53y8m | 2021-04-15 09:14:30 | ||||
|
Ampure bead clean up for high molecular weight DNA Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.6kphcvn | Sullivan Lab | The Ohio State University | 1 | 2020 | Natalie Solonenko 2020. Ampure bead clean up for high molecular weight DNA . protocols.io https://dx.doi.org/10.17504/protocols.io.6kphcvn | 2021-04-15 09:14:28 | ||||
|
DNA Preparation and Linker Amplification for Pyrosequencing Resource Report Resource Website |
Bonnie Poulos, Melissa Duhaime, Li Deng | DOI:10.17504/protocols.io.c9zz75 | VERVE Net, Sullivan Lab | Here, we adapt the linker amplified shotgun library (LASL) approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a “reconditioning PCR” step to increase yield and minimize late-cycle PCR artifacts. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent.Adapted from the Broad’s LASL Sanger Seq’g Protocol, and optimized for low template work. | 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 | Bonnie Poulos, Melissa Duhaime, Li Deng 2016. DNA Preparation and Linker Amplification for Pyrosequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c9zz75 | 2021-04-15 09:14:28 | |||
|
Roseobacter Screening Of Surface Waters For Viruses Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dbt2nm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Roseobacter Screening Of Surface Waters For Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dbt2nm | 2021-04-15 09:14:40 | ||||
|
Checking DNA Concentration with Agarose Gel Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c35yq5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Checking DNA Concentration with Agarose Gel. protocols.io https://dx.doi.org/10.17504/protocols.io.c35yq5 | 2021-04-15 09:14:32 | ||||
|
Most Probable Number (MPN) Counts of Cyanophages Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ddb22m | VERVE Net, Sullivan Lab | Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Most Probable Number (MPN) Counts of Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddb22m | 2021-04-15 09:14:51 | |||
|
RNA Samples Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dev3e5 | 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. RNA Samples Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.dev3e5 | 2021-04-15 09:14:34 | |||
|
Ascorbic Acid Antifade Solution Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c87zzm | VERVE Net, Sullivan Lab | For use in 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. Ascorbic Acid Antifade Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c87zzm | 2021-04-15 09:14:56 | |||
|
EGTA tetrasodium salt Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c3pymm | VERVE Net, Sullivan Lab | For use in DNase I Treatment protocol for DNase inactivation | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Matthew Sullivan 2015. EGTA tetrasodium salt. protocols.io https://dx.doi.org/10.17504/protocols.io.c3pymm | 2021-04-15 09:14:39 | |||
|
Processing a Viral Metagenome Using iVirus Resource Report Resource Website |
Benjamin Bolduc | DOI:10.17504/protocols.io.ev3be8n | Sullivan Lab | 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. | Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB, iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal 11(1). doi: ismej201689 | The Ohio State University | https://www.nature.com/articles/ismej201689.pdf?origin=ppub | 1 | 2016 | Benjamin Bolduc 2016. Processing a Viral Metagenome Using iVirus. protocols.io https://dx.doi.org/10.17504/protocols.io.ev3be8n | 2021-04-15 09:15:09 | |
|
MTN100 with 1x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.def3bm | VERVE Net, Sullivan Lab | This mixture is is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 1x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.def3bm | 2021-04-15 09:14:44 | |||
|
Purifying Viruses Using Sucrose Cushion Resource Report Resource Website |
Shannon Williamson | DOI:10.17504/protocols.io.c3wypd | VERVE Net, Sullivan Lab | This protocol describes the use of a sucrose cushion to purify viruses. It is the Matthew Sullivan Lab adaptation of the Shannon Williamson protocol.DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012.Citation: Hurwitz, B. L., Deng, L., Poulos, B. T., & Sullivan, M. B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology. doi:10.1111/j.1462-2920.2012.02836.x | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | Shannon Williamson 2015. Purifying Viruses Using Sucrose Cushion. protocols.io https://dx.doi.org/10.17504/protocols.io.c3wypd | 2021-04-15 09:15:13 | |||
|
Screening Recombinant Clones by PCR Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c48yzv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. Screening Recombinant Clones by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.c48yzv | 2021-04-15 09:14:49 | ||||
|
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 |
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
