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Authors: JB Waterbury & JM Willey
Group: VERVE Net, Sullivan Lab
Summary: Reference: JB Waterbury & JM Willey. Isolation and growth of marine planktonic cyanobacteria. 1988. Methods in Enzymology 167: 100-105.
Proper citation: JB Waterbury & JM Willey 2016. SN Maintenance Medium for Synechococcus. protocols.io https://dx.doi.org/10.17504/protocols.io.c9hz35 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol provides a method to study phage-bacteria interactions by generating a Network in Cytoscape using the application CoNet. To CoNet tutorial can help with analysis. 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 P9: Phage-Bacteria Interaction Network. protocols.io https://dx.doi.org/10.17504/protocols.io.egybbxw Copy
Authors: Irina Agarkova
Group: VERVE Net
Proper citation: Irina Agarkova 2016. Recovery of DNA from Low Melting Point Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.et2beqe Copy
Authors: Ed DeLong
Group: VERVE Net, DeLong Research Group, SCOPE
Summary: This protocol is an update of the Metatranscriptomics protocol from DeLong lab 2012 which incorporates ScriptSeq v2 RNA library preparation.Part A: RNA extraction, DNase treatment, purification, and quantification.Part B: rRNA subtractionPart C: cDNA synthesis and Illumina library prep
Proper citation: Ed DeLong 2015. Metatranscriptomics sample preparation protocol w/ScriptSeq. protocols.io https://dx.doi.org/10.17504/protocols.io.dib4am Copy
Authors: Ken Youens-Clark
Group: VERVE Net, Hurwitz Lab
Proper citation: Ken Youens-Clark 2016. Adding data to iPlant/CyVerse Data Store. protocols.io https://dx.doi.org/10.17504/protocols.io.ehibb4e Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines the analysis used to plot contig coverage stats, as well as sequence count and length stats. We begin with visualizing contig length vs coverage. We then visualize the distributions of sequence counts per sample as a probability density plot (similar idea as a histogram), and then do the same for median sequence length. 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 R2: Whole Metagenome Contig and Sequencing Statistics. protocols.io https://dx.doi.org/10.17504/protocols.io.eh6bb9e Copy
Authors: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder
Group: VERVE Net
Summary: Using DGGE, similar-sized PCR products that differ in nucleotide composition (sequence) can be separated in denaturing gradient gels. Denaturing gradient gels are created using acrylamide (structural material) solutions that contain different amounts of denaturants (urea and formamide), such that the highest concentration of denaturants is at the bottom of the gel and the lowest concentration is at the top. As dsDNA fragments differing in sequence migrate into the gel during electrophoresis, they encounter increasing concentrations of denaturants, and each fragment partially melts (i.e., double-stranded regions dissociate into single-stranded) at a different place in the gel depending on its sequence. Because the electrophoretic mobility of partially melted DNA fragments is greatly reduced compared to dsDNA, same-sized DNA fragments with different sequences focus at different positions in these gels. Because PCR with universal primers can be used to amplify related, but different, DNA sequences, and different sequences focus at different positions in a denaturing gradient gel, DGGE can be used to produce a unique banding pattern, or fingerprint, for each PCR product amplified from different microbial communities.
Proper citation: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Fingerprinting aquatic virus communities using denaturing gradient gel electrophoresis (DGGE). protocols.io https://dx.doi.org/10.17504/protocols.io.dy37ym Copy
Authors: Dr. Steven Wilhelm
Group: VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs
Summary: Please contact Dr. Steven Wilhelm ([email protected]) with any additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm 2019. Typing E. coli ATCC 11303 with fluorescently stained virus.. protocols.io https://dx.doi.org/10.17504/protocols.io.iivcce6 Copy
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