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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. DNA Precipitation Protocol. protocols.io dx.doi.org/10.17504/protocols.io.c34yqv Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Modified after Glöckner et al. 1999
Proper citation: Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io dx.doi.org/10.17504/protocols.io.c3ayid Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of the trace metal mixture for addition to seawater for the cultivation of marine cyanobacteria, Prochlorococcus and Synechococcus
Proper citation: Matthew Sullivan Lab 2015. Cyanobacteria Trace Metal Mixture (CTMM). protocols.io dx.doi.org/10.17504/protocols.io.c8nzvd Copy
Authors: Chisholm Lab
Group: VERVE Net, Sullivan Lab
Proper citation: Chisholm Lab 2016. NATURAL SEAWATER-BASED PRO99 MEDIUM. protocols.io dx.doi.org/10.17504/protocols.io.c7zzp5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Plating Prochlorococcus and Synechococcus strains in top agarose for plaque assays. protocols.io dx.doi.org/10.17504/protocols.io.c3vyn5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. g23 T4-type (myovirus) PCR Protocol. protocols.io dx.doi.org/10.17504/protocols.io.dfq3mv Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
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 2017. Preparing Data for vContact from Proteins (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.gwdbxa6 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: Purpose: To test axenic cultures for purity. Protocol described in S. Bertillson, O. Berglund, D.M. Karl, S.W. Chisholm (2003). Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea. Limnol Oceanogr 48(5):1721-1731.
Proper citation: Bonnie Poulos 2016. Marine Purity Broth. protocols.io dx.doi.org/10.17504/protocols.io.ekrbcv6 Copy
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 dx.doi.org/10.17504/protocols.io.djn4md Copy
Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in the "FASP Kit Protocol-ORNL Developed for Bacteriophage"
Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Digestion Solution. protocols.io dx.doi.org/10.17504/protocols.io.dek3cv Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: Assembling actual reads from the Ocean Sampling Day (2014) using SPAdes, an assembler implemented in Cyverse.
Proper citation: Benjamin Bolduc 2016. Assembling Viral Metagenomic Data with SPAdes (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.evzbe76 Copy
Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
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 dx.doi.org/10.17504/protocols.io.eyhbft6 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.Quality trimming of reads is important!
Proper citation: Benjamin Bolduc 2016. Quality Control of Reads Using Trimmomatic (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.ewbbfan Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for Viruses (See guidelines for DNA Extraction).
Proper citation: Matthew Sullivan 2016. Cesium Chloride Gradients. protocols.io dx.doi.org/10.17504/protocols.io.c7dzi5 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol.
Proper citation: Matthew Sullivan 2016. Centrifuged Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.ddj24m Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Proper citation: Li Deng 2016. WH7803 PCR Protocol. protocols.io dx.doi.org/10.17504/protocols.io.dak2cv Copy
Authors: Adriana Alberti
Group: VERVE Net, Sullivan Lab
Summary: Protocol for preparation of short single and paired-end libraries from genomic dsDNA starting from low DNA quantity (up to 10 ng) for Illumina sequenincg. Developed by Adriana Alberti at Genoscope.
Proper citation: Adriana Alberti 2016. Low input Library Preparation for Illumina Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.ddq25v Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Can be used for diluting or resuspending phage preparations.
Proper citation: Matthew Sullivan 2015. Phage Buffer. protocols.io dx.doi.org/10.17504/protocols.io.c5ey3d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Host Range Protocols. protocols.io dx.doi.org/10.17504/protocols.io.dew3fd Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For use in Wet-mount Method for Enumeration of Aquatic Viruses
Proper citation: Matthew Sullivan 2016. Working Bead Solution. protocols.io dx.doi.org/10.17504/protocols.io.c84zyv Copy
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