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.
Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in "FASP Kit Protocol-ORNL Developed for Bacteriophage"
Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Iodoacetamide Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dej3cm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA Extraction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c32yqd Copy
Authors: James E. Thornton
Group: VERVE Net, Sullivan Lab, Culley Lab_ULaval
Summary: This protocol describes the preparation of and treatment with DNase I to degrade DNA in solutions containing iron chloride, EDTA–Mg ascorbate buffer, and cesium chloride. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012. We use this protocol primarily to remove free host and other contaminating DNA from phage preparations prior to extracting nucleic acid from the phage particles.
Proper citation: James E. Thornton 2015. DNase I Treatment. protocols.io https://dx.doi.org/10.17504/protocols.io.c3myk5 Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-Mount Method for Enumeration of Aquatic Viruses
Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Iron Chloride Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c8wzxd Copy
Authors: Gary Trubl, Natalie Solonenko, Yueh-Fen Li
Group: Sullivan Lab
Summary: Protocol for resuspending viruses from soils and sediments. See attached file for considerations, adaptations, and references. This version does not include CsCl purification, see version 2 for CsCl information.
Proper citation: Gary Trubl, Natalie Solonenko, Yueh-Fen Li 2018. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.tzzep76 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used for the DNA Extraction Protocol.
Proper citation: Matthew Sullivan 2016. CsCl purified phage lysate, Proteinase K, SDS. protocols.io https://dx.doi.org/10.17504/protocols.io.c68zhv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA/RNA Extractions from Sterivex Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c4bysm Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: 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.
Proper citation: Benjamin Bolduc 2016. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ewabfae Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: Protocol for labeling bacteria with N15. The bacterial DNA was made “heavy” so that community viral and host bacterial DNA could be distinguished from each other after sorting by using density gradient centrifugation.
Proper citation: Bonnie Poulos 2016. Isotopic Labeling of Cyanobacteria and DNA Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.c9nz5d Copy
Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly infected cells (FVIC), the frequency of infected cells (FIC), the fraction of mortality due to viral lysis (FMVL), and burst size.
Proper citation: Jennifer Brum 2016. FVIC (Frequency of Visibly Infected Cells) Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dbp2mm Copy
Authors: Ms Alex Aitken
Group: VERVE Net, Sullivan Lab
Summary: This shows how to make 0.5M EDTA
Proper citation: Ms Alex Aitken 2016. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c5wy7d Copy
Authors: Natalie Solonenko
Group: Sullivan Lab, Gene Flow in Subzero Brines
Summary: Adapted from Tara Oceans extraction protocol (see citation).
Proper citation: Natalie Solonenko 2018. Extracting Bacterial DNA from filters. protocols.io https://dx.doi.org/10.17504/protocols.io.qv8dw9w Copy
Authors: Qiagen
Group: VERVE Net, Sullivan Lab
Summary: This is a 0.05M Tris-Cl (pH 8.0), 0.01M EDTA resuspension buffer containing RNase A
Proper citation: Qiagen 2017. Resuspension Buffer P1. protocols.io https://dx.doi.org/10.17504/protocols.io.hxgb7jw Copy
Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab
Proper citation: Natalie Solonenko 2016. 16S PCR Universal. protocols.io https://dx.doi.org/10.17504/protocols.io.c5my45 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. One-Step Growth Curves for Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.dan2dd Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of trace metal stock solutions for cyanobacteria trace metal mixture (CTMM)
Proper citation: Matthew Sullivan Lab 2015. Primary trace metal stocks. protocols.io https://dx.doi.org/10.17504/protocols.io.c8hzt5 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Bonnie Poulos 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ek2bcye Copy
Authors: Faculty of Medicine Flow Cytometry Facility, U. of Toronto
Group: VERVE Net, Sullivan Lab
Summary: This is a guide to prepare PFA from powder. This is useful for PFA Fixation.
Proper citation: Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Paraformaldehyde (PFA) from Powder. protocols.io https://dx.doi.org/10.17504/protocols.io.c5yy7v Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: Preparing data for use in vContact by using VirSorted Ocean Sampling Day (2014) contigs, using tools available in Cyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this protocol are suitable for vContact-PCs.
Proper citation: Benjamin Bolduc 2016. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ev7be9n Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Sequence for barcoded oligos for linker amplified libraries. Numbers 1 to 29 were developed at the Tucson Marine Phage Lab dervied from MID 1 to 14 recommended by Roche.
Proper citation: Matthew Sullivan 2016. Barcode Oligos for Linker Amplified DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.ddp25m Copy
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:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
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 sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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
