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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: From Sullivan M., Lindell D., Lee J., Thompson L., Bielawski J., Chisholm S. Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.PLOS Biology, 2006 4(8):e234. Please see the published manuscript for additional information.
Proper citation: Matthew Sullivan 2016. Amplification of phage genes from lysates and environmental samples. protocols.io https://dx.doi.org/10.17504/protocols.io.djn4md Copy
Authors: DeLong Lab
Group: VERVE Net, Sullivan Lab
Proper citation: DeLong Lab 2015. Lysozyme & RNase A Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dje4jd Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2016. Preparation of Virus DNA from Seawater for Metagenomics. protocols.io https://dx.doi.org/10.17504/protocols.io.c28yhv Copy
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. Urea Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dei3cd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: .
Proper citation: Matthew Sullivan 2016. 0.7% Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.c7bzim Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Cellulophaga Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.dez3f5 Copy
Authors: Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: Collaborator, Nathan VerBerkmoes (Oak Ridge National Labs), worked with Tucson Marine Phage Lab to develop more sensitive proteomics assays for viral isolates which we are now also using for environmental viral concentrates. A new sample prep method (FASP) was optimized to maximize the signal from our commonly low-protein containing samples, and then run using 2d-LC-MS-MS to maximize detection across the large dynamic range in isolate and environmental samples.
Proper citation: Nathan VerBerkmoes 2016. FASP Kit Protocol-ORNL Developed for Bacteriophage. protocols.io https://dx.doi.org/10.17504/protocols.io.ddn25d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used with Cesium Chloride Dialysis for Viruses
Proper citation: Matthew Sullivan 2016. MTN100 with 5x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.ded3a5 Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: This medium is used successfully for most cyanobacteria. Vitamin B12 may be added for those species that require it. Use f/2 vitamin solution.
Proper citation: Li Deng 2016. BG-11 Medium for Freshwater Cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.ddd225 Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2015. Cyanophage plaque purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3yypv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is is used with Cesium Chloride Dialysis for Viruses
Proper citation: Matthew Sullivan 2016. MTN100 with 3x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.dee3bd Copy
Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab
Proper citation: Natalie Solonenko 2016. Isolation of DNA from phage lysate. protocols.io https://dx.doi.org/10.17504/protocols.io.c36yrd 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.Quality trimming of reads is important!
Proper citation: Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.eygbftw Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.der3d5 Copy
Authors: Natalie Solonenko, Marie Burris
Group: Sullivan Lab
Summary: This protocol details steps to prepare DNA for long-read library prep, including clean-up and shearing.
Proper citation: Natalie Solonenko, Marie Burris 2020. Preparation of extracted DNA for long-read library prep. protocols.io https://dx.doi.org/10.17504/protocols.io.6iyhcfw Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2015. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c58y9v Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.ek6bcze Copy
Authors: Seth John, Bonnie Poulos, Christine Schirmer
Group: VERVE Net, Sullivan Lab
Summary: This protocol describes a technique to recover viruses from natural waters using iron- based flocculation and large-pore-size filtration, followed by resuspension of virus- containing precipitates in a pH 6.5 buffer. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered if using oxalic acid in the resuspension buffer. Particles lose infectivity if resuspended with ascorbic acid in the buffer.
Proper citation: Seth John, Bonnie Poulos, Christine Schirmer 2015. Iron Chloride Precipitation of Viruses from Seawater. protocols.io https://dx.doi.org/10.17504/protocols.io.c2wyfd Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Formulation for a phosphate-buffered 20% glutaraldehyde stock solution.
Proper citation: Li Deng 2015. Buffered glutaraldehyde. protocols.io https://dx.doi.org/10.17504/protocols.io.c7gzjv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Calculating burst size. protocols.io https://dx.doi.org/10.17504/protocols.io.ddm245 Copy
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