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Authors: Mel Duhaime
Group: VERVE Net, Sullivan Lab
Proper citation: Mel Duhaime 2016. PSS2 PCR Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.dfm3k5 Copy
Authors: James Thornton
Group: VERVE Net, Sullivan Lab
Summary: For use in DNase I Treatment protocol for DNase inactivation.
Proper citation: James Thornton 2015. EDTA disodium salt dihydrate. protocols.io https://dx.doi.org/10.17504/protocols.io.dbm2k5 Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: Matthew Sullivan Lab 2015. Coring Technique. protocols.io https://dx.doi.org/10.17504/protocols.io.c3zyp5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. One-step growth curves for Cellulophaga phages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddh235 Copy
Authors: Shalaja Srinagesh et al
Group: VERVE Net, Sullivan Lab
Proper citation: Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbn2md Copy
Authors: Gary Trubl, Natalie Solonenko
Group: Sullivan Lab
Summary: Resuspend viruses from soils and sediments
Proper citation: Gary Trubl, Natalie Solonenko 2017. Soil viral extraction protocol for ssDNA & dsDNA viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.hu3b6yn Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan Lab 2016. Double SPRI for Second Generation Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c53y8m Copy
Authors: Natalie Solonenko
Group: Sullivan Lab
Proper citation: Natalie Solonenko 2020. Ampure bead clean up for high molecular weight DNA . protocols.io https://dx.doi.org/10.17504/protocols.io.6kphcvn Copy
Authors: Bonnie Poulos, Melissa Duhaime, Li Deng
Group: VERVE Net, Sullivan Lab
Summary: 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.
Proper citation: 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 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Roseobacter Screening Of Surface Waters For Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dbt2nm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Checking DNA Concentration with Agarose Gel. protocols.io https://dx.doi.org/10.17504/protocols.io.c35yq5 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner.
Proper citation: Bonnie Poulos 2016. Most Probable Number (MPN) Counts of Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddb22m 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. RNA Samples Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.dev3e5 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. Ascorbic Acid Antifade Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c87zzm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For use in DNase I Treatment protocol for DNase inactivation
Proper citation: Matthew Sullivan 2015. EGTA tetrasodium salt. protocols.io https://dx.doi.org/10.17504/protocols.io.c3pymm Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
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. Processing a Viral Metagenome Using iVirus. protocols.io https://dx.doi.org/10.17504/protocols.io.ev3be8n 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 1x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.def3bm Copy
Authors: Shannon Williamson
Group: VERVE Net, Sullivan Lab
Summary: 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
Proper citation: Shannon Williamson 2015. Purifying Viruses Using Sucrose Cushion. protocols.io https://dx.doi.org/10.17504/protocols.io.c3wypd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Screening Recombinant Clones by PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.c48yzv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Reverse Cross-linking Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c6bzam Copy
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