bluuebunny/crossref_metadata_2025 huggingface dataset:
QIIME:Moving Pictures of the human microbiome v1
Authors: Hurwitz Bonnie
Published: June 2017

This tutorial covers a full QIIME workflow using Illumina sequencing data and was adapted from a tutorial on the QIIME website.. This tutorial is intended to be quick to run, and as such, uses only a subset of a full Illumina Genome Analyzer II (GAIIx) run. We'll make use of the Greengenes reference OTUs, which is the default reference database used by QIIME. You can determine which version of Greengenes is being used by running print_qiime_config.py. This will be Greengenes, unless you've configured QIIME to use a different reference database by default.The data used in this tutorial are derived from the Moving Pictures of the Human Microbiome study, where two human subjects collected daily samples from four body sites: the tongue, the palm of the left hand, the palm of the right hand, and the gut (via fecal samples obtained by swapping used toilet paper). These data were sequenced using the barcoded amplicon sequencing protocol described in Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. A more recent version of this protocol that can be used with the Illumina HiSeq 2000 and MiSeq can be found here.
Installation and Getting Started v1
Authors: not provided Afiahayati , Sato K not provided , Namiki T not provided , Hachiya T not provided , Tanaka H not provided , Sakakibara Y. not provided
Published: June 2017

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 forde novometagenome 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, forde novometagenome 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.
VIROME: Downloading libraries of VIROME data v1
Authors: Bhavsar Jaysheel , Shawn Polson not provided , K. Eric Wommack not provided
Published: June 2017

This tutorial explainshow to download entire libraries of data from the VIROME web application. 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.
MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads v1
Authors: not provided Afiahayati , Sato K not provided , Namiki T not provided , Hachiya T not provided , Tanaka H not provided , Sakakibara Y. not provided
Published: June 2017

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 forde novometagenome 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, forde novometagenome 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.
Taxonomic biomarker discovery with LEfSe v1
Authors: Huttenhower Curtis
Published: June 2017

In this protocolwe show how to perform the taxonomic biomarker discovery operation using LEfSe.
MetaPhlAn profiling of 20 HMP samples v1
Authors: Huttenhower Curtis
Published: June 2017

In this protocolwe will show how to taxonomically profile 20 metagenomic shotgun samples Human Microbiome Project (HMP). Specifically, we will look at 10 samples from the buccal mucosa and 10 from the tongue dorsum. Please note these 20 samples are not necessarily an unbiased selection of microbiomes from the over 200 buccal mucosa and tongue dorsum samples generated by the HMP. REQUIREMENTS: BowTie2 installed and in the system path, Mercurial, basic unix commands (wget, tar). The size of the 20 samples (60GBs) can make their download quite slow. For this reason we are also providing the overall output of this protocol(few KBs) available for download so that one can start the tutorial from MetaPhlAn output merge and visualizationif needed.
Zymoclean™ Gel DNA Recovery Kit v1
Authors: J. Cone Alan
Published: June 2017

This is a protocol for high yield recovery of pure DNA from agarose gels using the Zymoclean™ Gel DNA Recovery Kit.
Centrifuged Sample Steps v1
Authors: Sullivan Matthew
Published: June 2017

For One-step growth curves for Cellulophaga phages protocol.
Non-Centrifuged Sample Steps v1
Authors: Sullivan Matthew
Published: June 2017

For One-step growth curves for Cellulophaga phages protocol.
Low input Library Preparation for Illumina Sequencing v1
Authors: Alberti Adriana
Published: June 2017

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.
MTN100 with 5x NaCl v1
Authors: Sullivan Matthew
Published: June 2017

This mixture is used with Cesium Chloride Dialysis for Viruses
Iodoacetamide Solution v1
Authors: Corrier/Nathan VerBerkmoes Kristin
Published: June 2017

For use in "FASP Kit Protocol-ORNL Developed for Bacteriophage"
Digestion Solution v1
Authors: Corrier/Nathan VerBerkmoes Kristin
Published: June 2017

For use in the "FASP Kit Protocol-ORNL Developed for Bacteriophage"
RNA Samples Steps v1
Authors: Sullivan Matthew
Published: June 2017

For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Acidified Distilled Water v1
Authors: Hall Sonia
Published: June 2017

Combine 2mls glacial acetic acid 1L distilled water
Weigert's Hematoxylin v1
Authors: Hall Sonia
Published: June 2017

Add an equal volume of Solution B to Solution A in the hood. Cover bottle with aluminum foil to reduce light exposure. Remake every month.
geneELISA for highthroughput examination of phage?host interactions v1
Authors: Sullivan Matthew , Sarah Schwenck not provided , Cristina Howard-Varona not provided , Vinh Dang not provided
Published: June 2017

Bacterial viruses (phages) influence global biogeochemical cycles by modulating bacterial mortality, metabolic output and evolution. However, our understanding of phage infections is limited by few methods and environmentally-relevant model systems. Prior work showed that Cellulophaga baltica phage ϕ38:1 infects its original host lytically, and an alternative host either delayed lytically or lysogenically. Here we investigate these infections through traditional and marker-based approaches, and introduce geneELISA for highthroughput examination of phage‒host interactions.
CsCl Step Gradient Buffer v1
Authors: King Jonathan
Published: June 2017

This mixture is used in the CsCl Step Gradient to Purify Phage Protocol
PBS-paraformaldehyde 8% v1
Authors: Sanchez Miguel
Published: June 2017

-I prepare 8% PFA (w/v) because I like to fix cells without even removing medium (because of the microtubules). If you want to use it 4% you can just dilute 1:1 with fresh PBS1X. - Usually prepare about 250ml batches each time so you'd need ~20g of paraformaldehyde. Both PFAs we have in the lab will work just fine; I prefer the posh one (TAAB pellets) because they are slightly higher grade and they do not form dust (very toxic). But the Sigma powder will work just fine as well. If you use Sigma powder, you should weigh it inside the fume hood too. - I first dilute and rise the pH to solubilize just in water. You may add a shorter volume (~150ml) to rinse later, after adding the pH correcting volumes. Remember that you'll also need a 10% volume (25ml in this example) of PBS10X at the end of the protocol!. Of course use mQ water. The mix will be very milky and acid at the start. Prepare in a suitable glass flask, I usually use a 2X volume Erlenmeyer. - Start mixing and heating moderately inside the fume hood. You may put a parafilm "cap" to minimise fumes and evaporation. Overheating (>55degrees) is to be avoided, use a thermometer if you don't trust your hand. If you play properly with pH, you won't have any trouble and won't need much heating, not even when using the pellets. - Add NaOH (I would recommend high concentrations, 10N) drop wise. Probably you'll need to add about 2mls until the soution clears. It usually takes about 20-30min. so be patient and wait for a while every time you add a small 250microl volume or so. - Once cleared, you can adjust the pH back from the very high (>10) you've got now, to what it should be (7-8), using HCl. Usually you need about 1ml of 1M HCl. - Once adjusted, you can rinse the total volume adding your 10% V of PBS10X and H2O. - Let cool before aliquoting and freezing. I usually freeze it as it is, and then always, before use upon thawing, I filter it with a .45micron. It's very normal after readjusting pH to have some tiny "fibbers" or aggregates; they won't change upon removal the effect of your fixation, but they will be a source of a lot of trouble (very bright autofluorescence, pH goes acid if they stay) if you don't filter.
Cellulophaga growth reading v1
Authors: Sullivan Matthew
Published: June 2017

For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Viruses from Sulfolobus and close relatives v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

The following methods are basically method “A” of Zillig et al. (1994) and were described recently in detail by Prangishvili (2006). These methods consist of enrichment cultures followed by host isolation and screening for virus production in both these isolates and enrichment cultures. These techniques are very similar to those used for bacteriophages, with the major exception being the extreme growth conditions (80˚C, pH 3). 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.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
Isolation of temperate phages by plaque agar overlay v1
Authors: H. Paul and Markus Weinbauer John
Published: June 2017

This protocol gives a method for isolating temperate phages from marine viral concentrations.This protocol uses the conventional plaque agar overlay and looking for turbid or haloed plaques, a hallmark of temperate phages. 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 full chapter for additional details.
Liquid Amplification v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Obtaining pure cyanophage stock: plaque purification"
Adsorption of phage to cyanobacteria v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

Several methods have been presented by Adams (1959) to determine adsorption kinetics of bacteriophages. One way to measure the adsorption efficiency of cyanophages is to assay for free unadsorbed phages (Suttle and Chan 1993). The principle of this assay is to add a known quantity of viruses to host cells (e.g., at an MOI = 0.01 to 0.1). Over a period of 1 to 2 h, small subsamples of the virus:host solution are removed ca. every 15 min and diluted 100-fold to stop further adsorption. The host is then separated from free viruses by centrifugation, and the number of free viruses remaining in the supernatant determined by plaque or end-point dilution assays. A plot of the abundance of free viruses remaining in solution as a function of time should produce a straight line. The slope of this line is then used to calculate the adsorption rate. This procedure can be adapted for other host–virus systems. The example given is for host BBC1 and cyanophage BBC1-P1 (Suttle and Chan 1993).
Construction of pGGDestTol2LC-sgRNA vectors v1
Authors: Yin Linlin , Lisette A. Maddison not provided , Mingyu Li not provided , Nergis Kara not provided , Matthew C. LaFave not provided , K. Varshney Gaurav , Shawn M. Burgess not provided , James G. Patton not provided , and Wenbiao Chen not provided
Published: June 2017

This protocols is from: Linlin Yin, et al.(2015) Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs.Genetics200:431-441;doi:10.1534/genetics.115.176917 Please see the full manuscript for additional details.
Release of nucleic acids with heat, chelator, and detergent v1
Authors: F. Steward and Alexander I. Culley Grieg
Published: June 2017

If one has a purified stock of viruses obtained, for example, by banding in a buoyant density gradient, or even a relatively pure viral concentrate obtained by size fractionation, it is possible to release the DNA in a high molecular weight form suitable for some applications (e.g., pulsed-field gel electrophoresis [PFGE] for sizing or probing, or nucleic acid quantificationby fluorescence) relatively simply. This method involves exchanging the buffer in which the viruses are suspended with one containing EDTA and SDS, followed by heating. The method is similar to that described previously (Steward 2001), but with the optional addition of detergent to facilitate disintegration of the viral capsid. This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
A degenerate primer reverse transcriptionpolymerase chain reaction protocol to determine the diversity of picorna-like viruses v1
Authors: I. Culley Alexander , Curtis A. Suttle not provided , and Grieg F. Steward not provided
Published: June 2017

The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known about the composition, dynamics, and ecology of the RNA virioplankton. In this protocol, we describe a method to assess RNA virus diversity from seawater.
Extracting nucleic acids from viruses on a filter v1
Authors: F. Steward and Alexander I. Culley Grieg
Published: June 2017

This protocol is a minor modification of that reported by Culley and Steward (2007). As the starting point for this protocol, we assume that viruses have been collected on an aluminumoxide 0.02-µm syringe-tip filter (Anotop, Whatman), but other filters capable of capturing viruses may be substituted. This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses.Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
HERP Insertion Mixture v1
Authors: G. Alexander William , Drew T. Doering not provided , and Chris Todd Hittinger not provided
Published: June 2017

This is part of the HERP protocol, from: Alexander WG, Doering DT,andHittinger CT (2014) High-Efficiency Genome Editing and Allele Replacement in Prototrophic and Wild Strains of Saccharomyces.Genetics 198:859-866;doi:10.1534/genetics.114.170118
Simultaneous measurement of grazing and viral lysis of phytoplankton v1
Authors: Brussaard Corina , Anne-Claire Baudoux not provided , Anna A. M. Noordeloos not provided , Marcel J. W. Veldhuis not provided
Published: June 2017

An adapted dilution method was used to estimate viral lysis and microzooplankton grazing simultaneously. Parallel dilution experiments were performed with 30 kDa ultrafiltrate (virus and grazer-free diluent) and 0.2 µm filtered seawater (grazer-free, but virus-containing diluent). Specific viral lysis rates were calculated from the difference in P. globosa growth rates between the 2 dilution series after 24 h incubation under natural conditions. The validity of this method was tested using a culture of P. globosa infected with a known P. globosa virus (PgV). Protocol derived from: Baudoux, A., Noordeloos, A., Veldhuis, M., & Brussaard, C. (2006). Virally induced mortality of Phaeocystis globosa during two spring blooms in temperate coastal waters. Aquat. Microb. Ecol. Aquatic Microbial Ecology,44(3), 207-217.
Bead Beating RNA extraction from 25 mm filter v1
Authors: Smith Christa
Published: June 2017

This protocol is for extracting RNA from 25 mm filters and can be used with filters stored in RNAlater for preservation. This protocol has been tested with 0.22 μm pore size Durapore filters. Custom synthesized RNA transcript standards are added at the time of extraction and are recovered post-sequencing for quantitative metatranscriptome analysis (Satinsky et al., 2013).
Anti-BrdU Staining Protocols Using DNAse with Surface and Fluorescent Proteins v1
Authors: Miller Kelsey
Published: June 2017

Anti-BrdU Staining Protocol using DNAse with surface and fluorescent proteins
MojoSort™ Isolation Kits No Wash Protocol v1
Authors: Miller Kelsey
Published: June 2017

Target cells are depleted by incubating your sample with the biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads (Cat. No. 480015/480016). The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells are collected. These are your cells of interest; do not discard the liquid. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.
MojoSort™ Human CD45 Nanobeads Protocol A v1
Authors: Miller Kelsey
Published: June 2017

Note: If the percentage of CD45+ cells in your sample is less than 50%, please follow Protocol A. If it is higher than 50% then please follow protocol B. The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc.
Tube-O-Dialyzer (No Loss Dialyzer for Small Samples) v1
Authors: not provided G-Biosciences
Published: June 2017

This protocol is forTube-O-DIALYZER™, a mini dialysis system for small sample volumes (20µl‐2.5ml). Follow this protocol for dialysis devicesCat. # 786‐610 to 786‐624.
ACUITYAdvanced Protocol v1
Authors: Miller Kelsey
Published: June 2017

ACUITYAdvanced Biotin Free HRPPolymer Detection System for Immunohistochemistry
MojoSort™ Human CD4 Nanobeads No Wash Protocol v1
Authors: Miller Kelsey
Published: June 2017

This protocol has been optimized to remove washing steps after antibody cocktail and nanobeads incubations, resulting in a shorter and more convenient protocol. This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube from human peripheral blood mononuclear cells (PBMCs). If working with fewer cells keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. To maximize the purity of CD4+ T cells we recommend the depletion of monocytes, as human monocytes express CD4. To deplete monocytes from human PBMCs, we recommend the use of MojoSort™ Human CD14 Selection Kit (Cat. No. 480025/480026). Alternatively, you may consider the Human CD4 T Cell Selection Kit (Cat. No. 480038). After monocyte depletion proceed to isolate the CD4+ T cells. You can also use other methods to deplete monocytes. If you wish to include monocytes in your CD4+ cell isolation, depletion is not required
OmniPrep™ For High Quality Genomic DNA Extraction From Ethanol- or Formalin-Fixed Tissue v1
Authors: not provided G-Biosciences
Published: June 2017

The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations. This protocol is for use with ethanol- or formalin- fixed tissue. Please refer to the appropriate protocol depending on your application.
CB-X™ Protein Assays Collection v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of protocols for theG-BiosciencesCB-X™ Protein Assay.
High sensitivity (low input) miRNA Illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit v7
Authors: Yip Karen , Kelvin Chan not provided , Danny Lee not provided
Published: June 2017

This protocol is designed for high sensitivity miRNA library generation for the Illumina sequencing platform. Our protocol and the enhanced reagent kit enables the discovery and profiling of small RNAs from a variety of sources including FFPE, exosome, serum, and whole blood. The TailorMix workflow is designed for ease of use, enabling library preparation a single day. Features: User Friendly Workflow: Libraries can be prepared in a single day. No Additional Reagents Necessary: All reaction enzymes and buffers are provided. Stress Free Gel Purification: TailorCut Gel Extraction Tool Set is included for easy gel excision and purification. Easy to Use: Reagents are supplied as ready-to-use mixtures which improves consistency and reproducibility. Ultra High Sensitivity: Prepare miRNA libraries from any source with as little as 10ng of total RNA input.
OmniPrep™ For High Quality Genomic DNA Extraction From Yeast v1
Authors: not provided G-Biosciences
Published: June 2017

The OmniPrep™ kit isolates high quality genomic DNA from many different species and tissue types including animal, plant, bacteria, yeast, fungi, whole blood, and cells in culture. DNA can be isolated from samples high in polysaccharides or other contaminants that are difficult to remove from the DNA preparations. This protocol is for use with yeast. Please refer to the appropriate protocol depending on your application.
XIT™ Genomic DNA Blood Kit Protocol for Purificaton of DNA from Amniotic Fluid v1
Authors: not provided G-Biosciences
Published: June 2017

This is a protocol forthe Isolation of Genomic DNA : PURIFICATION OF DNA FROM AMNIOTIC FLUID (Cat. # 786‐294, 786‐295, 786‐296)
Flex-T™ HLA Class I ELISA Protocol v1
Authors: Miller Kelsey
Published: June 2017

The HLA class I ELISA is an enzyme immunoassay based on the detection of β2-microglobulin subunit of HLA class I complexes, after capturing the complex through the conjugated biotin. To this end, biotinylated HLA class I complex is first captured in streptavidin coated microtiter wells. Subsequently, HRP-conjugated anti-human β2-microglobulin is added to detect intact HLA class I complexes. Only intact HLA class I complexes are recognized. Peptides with high affinity binding will be clearly detected by this ELISA technique, while peptides with a moderate to low binding affinity for HLA class I provide a moderate to non-detectable signal. This protocol is designed to evaluate the efficiency of peptide exchange when using the Flex-T™ system.
TCBS Agar Plates (500ml) v1
Authors: Hessen-Schmidt Sarah
Published: June 2017

Procedure for making TCBS Agar plates for selection of Vibrio bacteria
MegaLong™ Protocol for Isolation of >100kb Genomic DNA (Cell Culture) v1
Authors: not provided G-Biosciences
Published: June 2017

MegaLong™ isolates high molecular weight (>100kb) genomic DNA from a variety of samples, including animal tissues, cultured cells, whole blood, bacterial and yeast. The protocol described here is for cell culture samples. Please refer to the appropriate protocol, depending on your application.
Diatom Chloroplast Isolation Steps v1
Authors: Dreux Chappell P. , Bethany D. Jenkins not provided
Published: June 2017

A protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
Electron microscopy for virus identification and virus assemblage characterization v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

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.2010.978-0-9845591-0-7 Please see the published manuscript for additional information.
PCTE Protocol for VLP enumeration v1
Authors: Stedman Ken , Geoffrey Diemer not provided , Jennifer E Kyle not provided
Published: June 2017

An alternative epifluorescence microscopy (EFM) technique for virus enumeration has been developed using polycarbonate Track Etch (PCTE) filter membranes in place of aluminum oxide Anodisc membranes. The established EFM technique, first developed by Hennes and Suttle in 1995 and later expanded upon by Noble and Fuhrman in 1998, uses supported 20 nm pore-size Anodisc filter membranes to determine virus abundance in natural environments. Increased price and sporadic availability of Anodisc filters stimulated the evaluation of alternative filters for use in the procedure. The feasibility of using 30 nm pore-size PCTE filters for virus enumeration was assessed using the Anodisc filter procedure as a control. Although virion particle counts are slightly less precise using PCTE filters, they offer a substitute for Anodiscs while requiring only minor adjustments to the established protocol. Per slide, the PCTE costs approximately ten times less to prepare than the Anodisc-based method.
QIIME: VIROME comparinator tool diversity metrics v1
Authors: Ferrell Barbra
Published: June 2017

Viral Informatics Resource for Metagenome Exploration (VIROME) is a bioinformatics pipeline that classifies viral metagenome sequences after searching against annotated reference sequence databases (i.e., UniRef, SEED, ACLAME, COG, GO, KEGG, and PhageSEED) and a custom environmental database, Metagenomes Online (MgOl). VIROME’s compare tool allows users to compare any number of metagenomes to one another by generating a Biological Observation Matrix (biom) file that contain counts of occurrences of custom observations (comparison metrics), and a mapping text file that provides per-sample metadata (library IDs and descriptions). Quantitative Insights Into Microbial Ecology (QIIME) is an open-source software pipeline that allows users to interpret raw sequencing data and create graphical displays to interact with the data. QIIME is modular, providing users with the flexibility to select and integrate various applications. While QIIME has many capabilities and online tutorials, this SOP is limited to the steps a user will take to use VIROME’s compare tool output (biom and mapping files) to explore composition (what is in a sample), alpha-diversity (diversity within a sample), and beta-diversity (comparison of diversity between samples). This SOP generally follows guidance in online tutorials but with modifications unique to the VIROME Comparinator output analysis.
VBRC Base By Base: Switching between Mouse Modes v1
Authors: Tang Nick
Published: June 2017

Viral Bioinformatic Resource Centre Provide databases of viral genomic information. Please check theOrganismsmenu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (seeVBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation
VBRC Base By Base: Align entire sequences or subsequence regions v1
Authors: Tang Nick
Published: June 2017

Viral Bioinformatic Resource Centre Provide databases of viral genomic information. Please check theOrganismsmenu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (seeVBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation
Running PCPipe (protein clustering) in iPlant v1
Authors: Hurwitz Bonnie , Ken Youens-Clark not provided
Published: June 2017

Hurwitz, Bonnie L., and Matthew B. Sullivan. "The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology."PLoS One8.2 (2013): e57355.
Microbubbling technique v1
Authors: Sullivan Matthew
Published: June 2017

For use in the protocol "Large Volume Marine Cyanophage protocols"
Script P12: Antibiotic Resistance v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method for analysis of the relative abundance of potential antibiotic resistance genes found in the virome. We use the Comprehensive Antibiotic Resistance Database (CARD) as our reference for potential antibiotic resistance genes.
Script R4: Virome Taxonomy v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines our bacteriophage/virus taxonomy analyses. This analysis includes profiles for the average order relative abundance for each site, the phage species relative abundance profiles for each patient, and the relative abundance of specific species between sites. Intermediate files are also included with the publication, and the paths are specified below. 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."mBio6.5 (2015): e01578-15.
Script R5: Virome Alpha Diversity v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. 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."mBio6.5 (2015): e01578-15.
Script R6: Virome Beta Diversity v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the Bray-Curtis dissimilarity NMDS ordination and significance analysis of our manuscript. Here we will look at the clustering of the virome samples using our reference independent OTU table based on contig hits. We will compare skin environments (sebaceous, etc), occlusion status, and time. We also look at the difference between the background controls and the rest of the samples. 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."mBio6.5 (2015): e01578-15.
Script R13: OPF and AMG Analysis v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocolsoutlines our definitions of core operational protein families (OPFs), potential auxiliary metabolic genes (AMGs), sharing of genes across anatomical sites, and Bray-Curtis dissimilarity of the OPFs by anatomical site. Based on 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."mBio6.5 (2015): e01578-15.
Script R16: CRISPR Analysis v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines how to generate tables to analyze CRISPR interactions. Based on 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."mBio6.5 (2015): e01578-15.
Stellaris® RNA FISH Cells in Suspension Protocol v1
Authors: Biosearch Technologies LGC
Published: June 2017

Stellaris® RNA FISH Cells in Suspension Protocol is specifically optimized to allow to visualization of single RNA transcripts in suspended, fixed cells.
Resolving gel buffer (4X) v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.
CviRI Buffer A v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
10X MOPS Buffer v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in Preparation of Denaturing Agarose Gel for RNA Analysis.
Train for a One-Way Mission to Mars v1
Authors: Dion Edmond
Published: June 2017

This mock protocol is a fun description of the steps one might undertake to train for a one-way mission to the planet Mars. The One-Way mission concept is gaining popularity due to it's simpler approach and lower cost. Rather than expend effort to bring back the Marstronauts, the plan calls for leaving them there and ultimately colonizing the red planet.
Formulation of MBBM (Modified Bold's Basal Medium) v1
Authors: Dunigan and Irina Agarkova David
Published: June 2017

This medium is for growing Chlorella variabilis NC64A, Chlorella heliozoae SAG 3.83, and Coccomyxa C-169.
Bottle cleaning procedure for dissolved cobalt analyses v1
Authors: Bundy Randelle , Mak Saito not provided , Nick Hawco not provided , Abigail Noble not provided
Published: June 2017

This is a widely used cleaning procedure for trace metal clean analyses. This procedure is specifically for the bottles used for measuring dissolved and labile cobalt using cathodic stripping voltammetry.
Mapping Metagenomic Reads to Reference Sequences (Cyverse) v1
Authors: Bolduc Benjamin
Published: June 2017

Mapping metagenomic reads fromOcean Sampling Day (OSD) 2014 against NCBI's ViralRefSeq alongside viral sequences identified from the Tara Oceans survey using VirSorter.
In vitro transcription of guide RNAs v5
Authors: Dewitt Mark , Julia Wong not provided
Published: June 2017

sgRNA template assembly, in vitro T7transcription, andSPRI bead cleanup
Immunohistochemistry Protocol for Frozen Sections v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

The following is a general procedure guide for preparation and staining of acetone-fixed frozen tissues using a purified, unconjugated primary antibody, biotinylated secondary antibody and streptavidin-horseradish peroxidase (Sav-HRP) and DAB detection system. Because each antigen differs in terms of requirement for fixation, amplification step, etc., it is not possible to write an inclusive protocol that will work for all antigens. The user must determine optimal conditions for each antigen of interest. Many protocols for staining individual antigens, as well as useful tips and troubleshooting guides for immunohistochemistry, can be found at the IHC World web site (http://www.ihcworld.com/).
Immunohistochemistry Protocol for Paraffin-Embedded Sections v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

The following is a general procedure guide for preparation and staining of formalin-fixed, paraffin-embedded tissues using a purified, unconjugated primary antibody, biotinylated secondary antibody and streptavidin-horseradish peroxidase (Sav-HRP) and DAB detection system. Because each antigen differs in terms of requirement for fixation, amplification step, etc., it is not possible to write an inclusive protocol that will work for all antigens. The user must determine optimal conditions for each antigen of interest. Many protocols for staining individual antigens, as well as useful tips and troubleshooting guides for immunohistochemistry, can be found at the IHC World web site (http://www.ihcworld.com/).
Polarization of Mouse CD4+ Cells v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is collection of BioLegend protocols for polarization of mouse CD4+ cells. Please make sure you refer tothe correct protocol, depending on whether you are using Th1, Th2, Th17, or Treg.
True-Nuclear™ Transcription Factor Staining Protocols v1
Authors: not provided BioLegend , Inc. not provided
Published: June 2017

This is a collection of BioLegend protocols forTrue-Nuclear™ Transcription Factor Staining Protocols. Please make sure to refer to the correct protocol, depending on whether you are using the96-Well, U-Bottom Plate or 5 mL tubes.
One-step Phage Infection of Cyanobacteria (large-scale) v3
Authors: Giuliani Sarah
Published: June 2017

Experiment purpose: measure dynamics of phage infection and gene expressionincyanobacteria. We collect samples every 1-2 hours over a 12 hour period, starting froman initialinfection volume of 200ml per replicate per treatment.
MG_HW6: Gene Calls with Prodigal v1
Authors: Thornton James
Published: June 2017

This protocol provides the procedure to generate gene calls on your contigs using Prodigal.
Genomic DNA removal and total RNA purification from all types of lysate (ISOLATE II Biofluids RNA Kit) v1
Authors: not provided Bioline
Published: June 2017

The ISOLATE II Biofluids RNA Kit is specially developed for the rapid phenol-free isolation of high quality total RNA from biofluids and viruses. The following protocol is two part. The first part provides a procedure for the removal of genomic DNA applies to all the different types of lysate. Ensure you use the correct column: the Genomic DNA Removal Column has a blue ring. The second part is the protocol for the purification of total RNA apply to all the different types of lysate. Ensure you use the correct column: the ISOLATE II RNA Column has a black ring.
Lysate Preparation from Biofluids/Viruses v1
Authors: not provided Bioline
Published: June 2017

The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases. This protocol is designed for the isolation of all sizes of RNA (including miRNA) from a wide variety of biofluids such as saliva, urine, semen, CSF and blood. We recommend the use of non-coagulated blood samples (including fresh and anticoagulant treated blood). Follow this protocol for isolating viral RNA from biofluids. See here for isolating total RNA or viral RNA from plasma or serum.
Concatenated Tree Construction Demo: Identify Marker Genes v1
Authors: Dombrowski and Kiley Seitz Nina
Published: June 2017

Demo for identifying marker genes usingRiboDB.
Nutrient deplete/replete algal culture for elemental analysis v1
Authors: Zimmerman Amy
Published: June 2017

Purpose: To evaluate the influence of nutrient availability on cellular elemental composition (quotas and stoichiometry) in marine picoeukaryotes. Summary: Elemental quotas and ratios are assessed under nutrient replete and deplete conditions at the same time to minimize potential variation between experiments. Cells from an exponentially growing culture are concentrated by centrifugation, washed and re-suspended in a small volume of nutrient deplete media. These concentrated cells are used to inoculate triplicate replete and deplete culture flasks at a starting density corresponding to early-exponential growth. Culture growth is monitored daily. When the mean growth rate of the nutrient deplete treatment is half or less of the replete treatment (GRDEP/GRREP < 0.5), samples for cell counts and elemental analyses (dissolved nutrients; particulate carbon, nitrogen, and phosphorus) are collected.
Protoplast Isolation - Enzyme Buffer v1
Authors: Burgess Steven
Published: June 2017

Enzyme solution for the isolation of protoplasts suitable for Arabidopsis thaliana and Nicotiana benthamiana. Adapted from Yoo et al. 2007http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.199.html And excellent video from the Sheen Lab is available:https://www.youtube.com/watch?v=5-xm1EoLrW4
Beijerinck's Solution v1
Authors: Burgess Steven
Published: June 2017

Salt solution used in preparation of minimal medium for Chlamydomonas reinhardtii. Source: Sueoka, N. (1960) Proc. Natl. Acad. Sci. USA 46, 83-91. http://www.chlamycollection.org/Sueoka.html
TES v1
Authors: Miller Darach
Published: June 2017

From http://depts.washington.edu/younglab/yeastprotocols%28htm%29/RNA.htm
Sampling for qEXT and MPN assays: Large-scale One-step Phage Infection of Cyanobacteria v1
Authors: Giuliani Sarah
Published: June 2017

15 Hourly Timepoints: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 Sampling is for qPCR assay to determine total extracellular phage (qEXT) and MPN (most probable number) assay to determine % phage infectivity. For qEXT and MPN sampling, 250 µL of sample in duplicates were collected and filtered through a 0.2 µm, 96-well filter plate, for each time point. (Flow through filtrate containing phage is the sample to analyze).
Sampling for Flow Cytomtery (FCM) Cell Quantification: Large-scale One-step Phage Infection of Cyanobacteria v1
Authors: Giuliani Sarah
Published: June 2017

Experiment purpose is to monitor the time-course of a large-scale infection of host cyanobacteria by phage under variable media conditions and obtain samples for proteomic and transcriptomic analysis. 8 Hourly Timepoints: 0, 2, 4, 6, 8, 10, 12, 14 Sampling is to determine total cell concentration by flow cytometry. For Flow cytometry, 100 µl of sample in duplicate were taken from each experiment bottle at every other time-point and diluted 10 X in ASW salts, followed by fixing the sample by adding 5 µl of 25% glutaraldehyde, incubating in dark for about 10 minutes, and then flash freezing in liquid nitrogen. Samples were stored at -80°C for further processing.
ECOGEO 'Omics Training: 3.1 Amplicon Analysis - Mothur v2
Authors: Tully Ben
Published: June 2017

mothur is a bioinformatics tool for analyzing 16S rRNA gene sequences, which can be used to process data generated by Sanger, PacBio, IonTorrent, 454, and Illumina (MiSeq/HiSeq).
ECOGEO 'Omics Training: 4.2 Annotation v2
Authors: Seshadri Rekha
Published: June 2017

Introduction to functional annotation and Integrated Microbial Genomes (IMG) at the Joint Genome Institute (JGI). Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window.
Unix and Bioinformatics v3
Authors: Tully and Ken Youens-Clark Benjamin
Published: June 2017

This protocol details the use of various unix commands commonly used in bioinformatics.
ECOGEO 'Omics Training: Introduction to Environmenal 'Omics using a Unix-based Virtual Machine v1
Authors: M. Wood-Charlson Elisha
Published: June 2017

Before starting, please visit the ECOGEO website for more information on this 'Introduction to Environmental 'Omics' training series. The site contains a pre-packaged virtual machine (developed by Dr. Benjamin Tully, USC) that can be downloaded and used to run all of the protocols in this protocols.io collection. In addition to the VM, the website contains videos and presentations from our initial 'Introduction to Environmental 'Omics' workshop held at the Univ. of Hawai'i at Manoa on 25-26 Jul 2016.Please email ‘ecogeo-join@earthcube.org’ to join the ECOGEO listserv for future updates. Attached documentation includes an informational flyer, workshop agenda and participant list.
Mojosort™ Mouse Neutrophil Isolation Kit Protocol v1
Authors: Miller Kelsey
Published: June 2017

Non Neutrophil cells are depleted by incubating the sample with the biotin antibody cocktail followed by incubation with magnetic Streptavidin Nanobeads. The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells are collected. These are the cells of interest; do not discard the liquid. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.
Plant Pathogen Cultivation v1
Authors: Stam Remco
Published: June 2017

Collection of growth media and protocols to cultivate and harvest spores from several plant pathogens.
Non-Interfering™ (NI) Protein Assay Protocols v1
Authors: not provided G-Biosciences
Published: June 2017

This is a collection of Non-Interfering™ (NI) Protein Assay protocols from G-Biosciences.
Downloading SRA data using the SRA toolkit v1
Authors: Thornton James
Published: June 2017

The Sequence Read Archive (SRA) is a database for biological sequence data and ismaintained by the National Center for Biotechnology Information (NCBI). Sequence files can be obtained by using the SRA Toolkit. This protocol provides the stepsnecessary to use the SRA toolkit to get sequence data in fastq format.
Command line exercises with yeast v3
Authors: Youens-Clark Ken
Published: June 2017

Yeast is a well-characterized genome due to its small size and historical significance in genetics. The websitehttp://yeastgenome.org/ is a dedicated resource for yeast genomics.