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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stocks (liquid assay)"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Lysate titer. protocols.io dx.doi.org/10.17504/protocols.io.dqn5vd 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: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. DNA Gels. protocols.io dx.doi.org/10.17504/protocols.io.erubd6w Copy
Authors: John H. Paul and Markus Weinbauer
Group: VERVE Net
Summary: These are protocols from: Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the published manuscript for additional information.
Proper citation: John H. Paul and Markus Weinbauer 2016. Detection of Lysogeny in Marine Environments. protocols.io dx.doi.org/10.17504/protocols.io.ebjbakn 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: Bonnie Hurwitz, Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Summary: PCPipe is a protein-clustering tool. The input is a set of ORFs and a FASTA file with already clustered ORFs. The process entails:Use cd-hit-2d to compare the input peptides to previously clustered proteinsThe result is a file with input proteins that clustered to existing clusters and those that did notUse the unclustered peptides and self-cluster them via cd-hitTake a representative sequence from each novel cluster, and use "blastp" to compare to SIMAP.Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations fileProvide the user with two cluster files and the annotations for the new clusters based on the representative sequenceCode is freely available at Github.
Proper citation: Bonnie Hurwitz, Ken Youens-Clark 2016. PCPipe: Protein clustering with SIMAP annotations. protocols.io dx.doi.org/10.17504/protocols.io.ehfbb3n Copy
Authors: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Group: VERVE Net, Hurwitz Lab
Summary: Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome.Methods:We modified and extended a single-genome and de Bruijn-graph based assembler, Velvet, for de novo metagenome assembly. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.
Proper citation: Afiahayati, Sato K, Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2016. Installation and Getting Started. protocols.io dx.doi.org/10.17504/protocols.io.d5k84v Copy
Authors: Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen
Group: VERVE Net
Summary: This protocol is from:Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB (2008) Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation. PLoS Genet 4(6): e1000106. doi:10.1371/journal.pgen.1000106Please see the full manuscript for additional details.(Image: calf, Jim Champion, CC BY-SA)
Proper citation: Emily E. Hare, Brant K. Peterson, Venky N. Iyer, Rudolph Meier, Michael B. Eisen 2015. Eisen Lab, Fresh Cow Dung. protocols.io dx.doi.org/10.17504/protocols.io.ebebaje Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Chlorovirus Purification. protocols.io dx.doi.org/10.17504/protocols.io.er2bd8e Copy
Authors: Jozef Nissimov
Group: VERVE Net, Bidle Lab
Summary: Purification of viruses via CsCl gradient and ultracentrifugation
Proper citation: Jozef Nissimov 2015. Purification of viruses via CsCl gradient and ultracentrifugation. protocols.io dx.doi.org/10.17504/protocols.io.d9k94v 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: Hannigan GD, Grice EA, et al.
Group: VERVE Net, Club Grice
Summary: This protocol provides methods for quality control of metagenomic data. Included is adapter trimming, quality trimming, decontamination, negative control removal, and pre-processing results. Based on the methods found in the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: Hannigan GD, Grice EA, et al. 2016. Script P1: Pre-Processing Samples. protocols.io dx.doi.org/10.17504/protocols.io.edrba56 Copy
Authors: Dr. Steven Wilhelm, Samantha Coy
Group: VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Ultracentrifugation in the WX Ultra Series can support only 30 mL samples at a time, and therefore do not significantly concentrate viruses. Tangential flow filtration enables viral concentration of large volumes that can then be purified using sucrose density gradients. Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io dx.doi.org/10.17504/protocols.io.hgrb3v6 Copy
Authors: Priorclave
Group: VERVE Net
Summary: This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.Timing is everything when preparing a large meal. Unfortunately, for the truly epic holiday meals – like Thanksgiving – there never seems to be enough oven space to ensure everything arrives at the table steaming. Something has always cooled, collapsed, or coagulated before the turkey is ready to carve.This is where the autoclave comes in: It’s built to hold loads at around 250 degrees Fahrenheit, and since it subjects them to twice normal atmospheric pressure, it tends to cut cooking times in half. Autoclave cook-time for a small to mid-sized turkey should be less than 2 hours.Wanna impress the in-laws this year? Bring home your favorite tabletop food-grade autoclave (not your Priorclave, though; those are research-grade autoclaves!) and put it to use on the big day.
Proper citation: Priorclave 2016. Thanksgiving Dinner Autoclave Style. protocols.io dx.doi.org/10.17504/protocols.io.ea9bah6 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to plot MEGAN taxonomic assignments. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.
Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script R9: Plotting Microbial Taxonomy from MEGAN. protocols.io dx.doi.org/10.17504/protocols.io.ejdbci6 Copy
Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: This protocol is based on Schleper et al. (1992) as modified by Stedman et al. (2003).This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information.
Proper citation: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2015. Electron microscopy for virus identification and virus assemblage characterization. protocols.io dx.doi.org/10.17504/protocols.io.eahbab6 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: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack
Group: VERVE Net, Hurwitz Lab
Summary: This tutorial explains how to use VIROME to discover novel genetic polymorphism from viral metagenome shotgun data. Wommack, K. E., J. Bhavsar, S. W. Polson, J. Chen, M. Dumas, S. Srinivasiah, M. Furman, S. Jamindar, and D. J. Nasko. 2012. VIROME: a standard operating procedure for analysis of viral metagenome sequences. Standards in Genomic Sciences 6:427-439 [PMC3558967] See site for more information.
Proper citation: Jaysheel Bhavsar, Shawn Polson, K. Eric Wommack 2016. Discovering novel genetic polymorphism using VIROME. protocols.io dx.doi.org/10.17504/protocols.io.d6p9dm Copy
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