bluuebunny/crossref_metadata_2025 huggingface dataset:
Lethal Phase - Immunohistochemistry v1
Authors: M. Hall Sonia
Published: June 2017

Experiment was conducted to determine the stage at which mutant embryos arrest their development. All Drosophila melanogaster lines were crossed to balancers with a YFP marker for unambiguous identification of mutant and non-mutant embryos. Embryos were collected on apple juice agar plates with a smear of yeast paste for 1hr and aged for 17 hours at 25°C. Embryos were fixed and stained as described by Fehon et al., 1991 using a modified rotational speed of 150rpm.
Modified Qiagen QIAprep Spin Miniprep v1
Authors: Crone Michael
Published: June 2017

Modified to try to get increased yields.
Purification of viruses from culture lysates v1
Authors: E. Lawrence and Grieg F. Steward Janice
Published: June 2017

Ultracentrifugation provides a means to concentrate, analyze, and purify viruses in solution, and therefore represents an invaluable tool for aquatic virologists. This protocol provides a method for purification of viruses from culture lysates from natural water samples.
Qiagen QIAprep Spin Miniprep Kit (27104 or 27106) with a microcentrifuge v1
Authors: not provided QIAgen
Published: June 2017

This is the protocol for QIAgen's QIAprep Spin Miniprep Kit (catalog numbers 27104 or 27106) with their newer version 2.0 spin columns. For more information about the kit, see https://www.qiagen.com/us/shop/sample-technologies/dna/dna-preparation/qiaprep-spin-miniprep-kit?cmpid=QVenSPP1404quartzySC#orderinginformation. For purification ofup to 20 μg molecular biology grade plasmid DNA Ready-to-use plasmid DNA in minutes Reproducible yields of molecular biology grade plasmid DNA Single protocol for high- and low-copy vectors Even higher yields with the High-Yield Supplementary Protocol Improved QIAprep 2.0 Spin Column GelPilot loading dye for convenient sample analysis The QIAprep Spin Miniprep Kit is designed for isolation of up to 20 μg high-purity plasmid or cosmid DNA for use in routine molecular biology applications, including fluorescent and radioactive sequencing and cloning. Even higher yields (up to 30 μg) can be achieved using the High-Yield Supplementary Protocol.
Detecting 16S rRNA Gene Fragments from a Metagenome to Assemble Full-Length 16S Sequences v1
Authors: Tully Benjamin
Published: June 2017

Goal: Identify 16S rRNA gene metagenomic fragments and create assembled full-length 16S rRNA sequences from fragments. Note 1 - As is this case with most bioinformatic processes, this is one of many possible methods, but has had successful results in the past Note 2 - This method is best applied to sequences that have been subjected to quality control as inhttps://www.protocols.io/view/Basic-Illumina-Sequence-Quality-Control-d4e8td
VIROME Tutorials v1
Authors: Bhavsar Jaysheel , Shawn Polson not provided , K. Eric Wommack not provided
Published: June 2017

A collection of tutorials for the VIROME 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]
Running VirSorter in iPlant Discovery Environment v1
Authors: Roux Simon , Francois Enault not provided , Bonnie L. Hurwitz not provided , Matthew B. Sullivan not provided
Published: June 2017

This protocol gives an introduction to running VirSorter in the iPlant Discovery Environment.
DNA extraction from fungal mycelium using Extract-n-Amp v1
Authors: U'Ren Jana
Published: June 2017

This is a modified protocol for extracting DNA from fungal myelium using the Sigma-Aldrich Extract-N-Amp Plant Kit published by J.M. U'Ren et al. (2016) Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). Molecular Phylogenetics and Evolution 98: 210-232.
Metabolic profiling with HUMAnN v1
Authors: Huttenhower Curtis
Published: June 2017

In this protocol, we perform a metabolic profiling of metagenomic datasets using HUMAnN applied to the 20 samples taxonomically profiledin the other protocols contained in this collection. Once the metabolic profile has been generated, the following protocolscan be performed: MetaPhlAn output merge and visualizations GraPhlAn visualization of single and multiple samples Taxonomic biomarker discovery with LEfSe
Purification of viruses via CsCl gradient and ultracentrifugation v1
Authors: Nissimov Jozef
Published: June 2017

Purification of viruses via CsCl gradient and ultracentrifugation
Virus nucleic acids extractions from 0.02 µm anotop filters v1
Authors: Nissimov Jozef
Published: June 2017

This protocol has been modified from the original method developed and reported by Steward and Culley (2010) and Mueller et al. (2014). As a starting point we assume that viruses have been collected from the environment on 0.02 µm syringe filters (Anotop, Whatman).
MetaPhlAn output merge and visualization v1
Authors: Huttenhower Curtis
Published: June 2017

In this protocol, we will merge the 20 profiled metagenomes in a table of relative abundances and visualize the table with a heatmap.
GraPhlAn visualization of single and multiple samples v1
Authors: Huttenhower Curtis
Published: June 2017

In this protocolwe describe some approaches to graphically represent single profiled samples or a merged table of relative abundances.
Immunohistochemistry Blocking Solution v1
Authors: M. Hall Sonia
Published: June 2017

To make 10ml of blocking solution: 10ml 1X PBS 100ul 10% Triton-100 100ul Normal Donkey Serum
Mounting Media for Immunohistochemistry - Drosophila v1
Authors: M. Hall Sonia
Published: June 2017

Mounting Media
Paraffin Embedding of Drosophila Pupal Tissues v1
Authors: M. Hall Sonia
Published: June 2017

Drosophila Tissue Processing for Paraffin Embedding modified by the Baehrecke Lab from published protocols by Ristifo and White, 1991 (Pubmed ID 1936557) and Muro et al., 2006 (Pubmed ID 16887831)
Fixation Solution - FAAG v1
Authors: M. Hall Sonia
Published: June 2017

(store at 4 degrees Celsius) 80% Ethanol 4% Formaldehyde 5% Acetic Acid 1% Glutaraldehyde Measured Instructions Total volume 250 ml FAAG: 200 ml 100% Ethanol 27.5 ml 37% Formaldehyde 12.5 ml Glacial Acetic Acid 10 ml 25% Glutaraldehyde (EM Grade)
Glycerol Stock v1
Authors: J. Cone Alan
Published: June 2017

Method to create a long-term stable store of organisms. Especially useful if you want to store already transformed versions of organisms to aid in future experiments.
Marine Purity Broth v1
Authors: et al. Bertillson
Published: June 2017

Purpose: To test axenic cultures for purity
Most Probable Number (MPN) Counts of Cyanophages v1
Authors: Poulos Bonnie
Published: June 2017

Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner.
Analysis of Viral Morphological Characteristics v1
Authors: Brum Jennifer
Published: June 2017

Purpose: This protocol describes how to analyze a natural aquatic virus sample using transmission electron microscopy (TEM). The purpose is to obtain the capsid diameter distributions of the viral assemblage, tail length distributions of the viral assemblage, and percentages of each viral morphotype in a sample. Note: Prior to using this protocol, deposit viruses from your sample onto a TEM grid using the protocol “Quantitatively Depositing Viruses onto TEM Grids” then stain the viruses using the protocol “Positive and Negative Staining of Viruses on TEM Grids”.
One-Step Transformation of Yeast v1
Authors: Cone Alan
Published: June 2017

Quick and easy method to transform a free plasmid into either budding or fission yeast.
MTN100 with 3x NaCl v1
Authors: Sullivan Matthew
Published: June 2017

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

For use in 'FASP Kit Protocol-ORNL Developed for Bacteriophage'
Centrifuged Plaque Assay Sample Steps v1
Authors: Sullivan Matthew
Published: June 2017

For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Isolation of cyanophages by liquid bioassays v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

Multiwell plates are convenient for isolating cyanophages from environmental samples using the liquid bioassay approach (Table 1). This protocol describesa typical procedure (96-well assay) used to detect and isolate cyanophages from marine samples that lyses Synechococcus sp. strain DC2 (also known as CCMP1334 or WH7803). Using this method, greater than 105 lytic phages per milliliter of seawater have been detected in the Gulf of Mexico (Suttle and Chan 1994) that lyses this permissive target host.
Base agar plates v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Isolation of cyanophages by plaque assays"
Plasmid Miniprep v1
Authors: Timmons Joshua
Published: June 2017

Northeastern's method for plasmid extraction and purification. From Thermo Scientific's GeneJET Plasmid Miniprep Kit
Prophage induction in marine Synechococcus v1
Authors: H. Paul and Markus Weinbauer John
Published: June 2017

This protocol gives a method for prophage induction in marine Synechococcus. 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.
Estimation of viral-induced phytoplankton mortality using the modified dilution method v1
Authors: A. Kimmance and Corina P. D. Brussaard Susan
Published: June 2017

The modified dilution assay aims to partition phytoplankton mortality into virus- versus grazing-induced fractions and has previously been applied to several different environments to determine viral lysis rates of natural phytoplankton. The method involves creating a gradient of both grazing and viral lysis by dilution with different proportions of grazer- and virus-free filtrate, and assessing the subsequent impact on phytoplankton growth rates. Kimmance, S. A., and C. P. D. Brussaard. 2010. Estimation of viralinduced phytoplankton mortality using the modified dilution method, p. 65–73. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.
Separation of free virus particles from sediments in aquatic systems v1
Authors: Danovaro and Mathias Middelboe Roberto
Published: June 2017

Thisprotocol is for the separation of free virus particles from sediments. It is from: Danovaro, R., and M. Middelboe. 2010. Separation of free virus particles from sediments in aquatic systems, p. 74–81. 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.
Extinction dilution cloning for isolation of viruses infecting protists v1
Authors: Nagasaki and Gunnar Bratbak Keizo
Published: June 2017

This is a detailed outline of the extinction dilution method from: Nagasaki, K., and G. Bratbak. 2010. Isolation of viruses infecting photosynthetic and nonphotosynthetic protists, p. 92–101. 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.
Propagation/Amplification of Lytic Agent v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Isolation of cyanophages by liquid enrichment assay"
Isolation of cyanophages by plaque assays v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

More than 40 years ago, Safferman and Morris (1963) used the plaque assay method to isolate the first cyanophage that infects a freshwater filamentous cyanobacterium, Plectonema boryanum. Since then, this approach has been used successfully to detect and isolate a number of different phages infecting marine Synechoccocus and Prochlorococcus (e.g., Suttle and Chan 1993; Waterbury and Valois 1993; Wilson et al. 1993; Sullivan et al. 2003). The advantages of this method are that results are easily interpreted as plaques formed on pigmented lawns can be easily identified. Since a plaque is the result of a single infection event, the virus can be easily purified and cloned.The first part of the procedures described as follows: (1) preparation of base plates and (2) preparation of top agar/agarose are applicable also for bacteriophage plaque assays.
Top agarose v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "Isolation of cyanophages by plaque assyays"
One-step growth experiments (cyanophages) v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on Synechococcus sp. BBC1 (Suttle and Chan 1993).
Remove unadsorbed phages v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

For use in "One-step growth experiments (cyanophages)"
Direct delivery CRISPR-HDR editing protocol for C. elegans v1
Authors: Paix Alexandre , Andrew Folkmann not provided , Dominique Rasoloson and Geraldine Seydoux not provided
Published: June 2017

This protocol is for purification of Cas9::NLSSV40::His6from: Paix A,Folkmann A,Rasoloson D, andSeydoux G (2015) High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR/Cas9 Ribonucleoprotein Complexes.Geneticsgenetics.115.179382; Early online July 17, 2015.doi:10.1534/genetics.115.179382 Please see the full manuscript for detail.
Phenol-chloroform extraction with ethanol precipitation v1
Authors: F. Steward and Alexander I. Culley Grieg
Published: June 2017

The traditional phenol extraction procedure, based on early work by Kirby (1957) and elaborated in most modern protocol compendia, yields very clean nucleic acids suitable for a variety of downstream applications. This extraction method is coupled with a routine alcohol precipitation step to allow buffer exchange, removal of trace amounts of chloroform, and concentration of nucleic acids (Sambrook and Russell 2001). 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.
Hybridized Chain Reaction Fluorescent in situ Hybridization (HCR-FISH) v1
Authors: Lab Ruby
Published: June 2017

Hybridized Chain Reaction Fluroescent In Situ Hybridization for squid tissue and colonized V. fischeri.
Construction of shotgun libraries from RNA virus assemblages v1
Authors: I. Culley Alexander , Curtis A. Suttle not provided , and Grieg F. Steward not provided
Published: June 2017

The following protocol is used to construct shotgun libraries from RNA virus assemblages. This method is designed to detect all RNA viruses, regardless of their genome orientation, and therefore provides a broader assessment of RNA virus diversity compared to the single-gene–based method described in "A degenerate primer reverse transcriptionpolymerase chain reaction–based protocol to determine the diversity of picorna-like viruses."
Seydoux Lab Cas9 injection mix v1
Authors: Paix Alexandre , Andrew Folkmann not provided , Dominique Rasoloson not provided , Geraldine Seydoux not provided
Published: June 2017

This is the injection mixture for one locus editing using home‐made Cas9
From siRNA to shRNA v1
Authors: Liu Vivian
Published: June 2017

This brief protocol shows you how easy it is to get shRNA from demostrated siRNA sequence. With these self-designed shRNA, I've got more than 10 genes knockdown from mammalian cell lines, including mouse embryonic stem cells. Believe it or not, using siRNA sequence from Dharmacon will guarantee you the success.
One Shot® TOP10 Chemically Competent E. coli Transformation v1
Authors: Cone Alan
Published: June 2017

This procedure allows you to transform DNA into chemically competetentE. coli.
Seamless editing of the C. elegans genome using CRISPR/Cas9 v1
Authors: Paix Alexandre , Yuemeng Wang not provided , Harold E. Smith not provided , Chih-Yung S. Lee not provided , Deepika Calidas not provided , Tu Lu not provided , Jarrett Smith not provided , Helen Schmidt not provided , Michael W. Krause not provided , and Geraldine Seydoux not provided
Published: June 2017

This protocols is from: Alexandre Paix, et al. (2014) Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans.Genetics198:1347-1356;doi:10.1534/genetics.114.170423 Please see the full manuscript or additional details
Isolation and life cycle characterization of lytic viruses infecting heterotrophic bacteria and cyanobacteria v1
Authors: Middelboe Mathias , Amy M. Chan not provided , and Sif K. Bertelsen not provided
Published: June 2017

This collection presents some of the most widely used methodological approaches for isolation and purification of bacteriophages and cyanophages, the first step in detailed studies of virus–host interactions and viral genetic composition, and discusses the applications and limitations of different isolation procedures. Most work on phage isolation has been carried out with aerobic heterotrophic bacteria and cyanobacteria, culturable both on agar plates and in enriched liquid cultures. The procedures presented here are limited to lytic viruses infecting such hosts. In addition to the isolation procedures, methods for life cycle characterization (one-step growth experiments) of bacteriophages and cyanophages are described.
Characterization of the diversity of marine RNA 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 collection, we describe two methods to assess RNA virus diversity from seawater.
CTAB mix v1
Authors: Baker Andrew
Published: June 2017

This solution is used in the coral genomic DNA extraction protocol. The following recipe is for 50 mL of CTAB mix. Store at -20°C.
Sodium acetate solution v1
Authors: Baker and Ross Cunning Andrew
Published: June 2017

Sodium acetate solution is used in DNA extraction. This recipemakes 50 mL of a 3 Mstock solution at ph 5.2 -- dilute tenfold in water to a working concentration of 0.3 M for use in the DNA extraction protocol.
TE Buffer v1
Authors: Baker Andrew , Ross Cunning not provided
Published: June 2017

This TE buffer contains 10 mM Tris and 0.1 mM EDTA for storage of nucleic acids. Concentration of EDTA is lower than other formulations of TE buffer so that EDTA will not inhibit Taq Polymerase in downstream PCR reactions.
Concentration of viruses and preparation of FLVs for tracer assays v1
Authors: M. Comeau and Rachel T. Noble André
Published: June 2017

The steps describe how to prepare each virus concentrate. There are multiple options for many of the steps; in the case where there is more than one option they are noted in annotations.
MojoSort™ Human CD45 Nanobeads Protocol B 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.
Anti-Neu5Gc Antibody Kit Protocol - Flow Cytometry v1
Authors: Miller Kelsey
Published: June 2017

Anti-Neu5Gc may be used for staining cells prior to analysis by Flow Cytometry. This kit contains all the essential components needed to identify Neu5Gc on the surface of cells by flow cytometry. Use of the blocking agent (Neu5Gc Assay Blocking Solution) provided in the kit is essential, as commonly used blocking agents invariably contain serum, or serum components, that can either inhibit detection or introduce Neu5Gc contamination. Tissue culture-grown CHO-K1 can be used as a positive control, and human peripheral blood mononuclear cells serve as a negative control. Adherent tissue culture-grown cells should be released from the culture flasks by using 5-10mM EDTA for 10 minutes at room temperature. Other non-enzymatic methods, such as Accutase, may be used. Immediately wash cells in blocking buffer that contains a lower concentration of EDTA, and resuspend cells in blocking buffer to determine cell numbers and viability.
Anti-Neu5Gc Antibody Kit Protocol - Western blot v1
Authors: Miller Kelsey
Published: June 2017

The Anti-Neu5Gc Antibody Kit contains the essential monospecific polyclonal chicken IgY antibody, along with a negative control primary antibody to detect the presence of Neu5Gc on glycoconjugates by Western blot (WB). Samples to be evaluated are first subjected to SDS-PAGE, followed by transfer to a nitrocellulose or polyvinylidenedifluoride (PVDF) membrane. The membrane is then incubated with affinity-purified polyclonal anti-Neu5Gc to determine the presence of Neu5Gc on the protein of interest. The antibody provided in this kit has been shown to identify as little as 5 pmol of Neu5Gc per ug glycoprotein, which is at or below the current detection limit for conventional analysis by acid release, purification, DMB derivatization, HPLC, and electrospray mass-spectrometry. The Western blot provides additional information in that it confirms that Neu5G is directly linked to the glycoprotein of interest rather than to an accompanying sample component.
MojoSort™ Nanobeads Regular Protocol v1
Authors: Miller Kelsey
Published: June 2017

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. Note: For Human CD4 Nanobeads, please refer to the protocol found on the product webpage for MojoSort™ Human CD4 Nanobeads (Cat. No. 480013/480014).
MojoSort™ Isolation Kits Regular 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 Protocols 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.
Red Blood Cell Lysis Protocols v1
Authors: Miller Kelsey
Published: June 2017

BioLegend’s Red Blood Cell (RBC) Lysis Buffer (Cat. No. 420301) has been designed,formulated, and tested to ensure optimal lysis of RBCs in single cell suspensionsof hematopoietic tissues, such as spleen, as well as RBCs derived from peripheralblood. RBC Lysis Buffer contains ammonium chloride, which has been demonstratedto lyse RBCs with a minimum of harmful effects on lymphocytes
Generating CB-X™ Tables and standard curves for CB-X Protein Assay Optimization v1
Authors: not provided G-Biosciences
Published: June 2017

For routine protein assays, we recommend that researchers generate their own CB-X™ Tables or standard curves. This is a one time commitment to ensure user specific results and allows single tube assays to be performed each time as opposed to generating new calibration plots for each assay. We recommend using a protein standard similar to you protein of interest or a purified source of your protein. The supplied CB-X™ tables may result in some inconsistencies due to the type of cuvettes or microtiter plates used. CB-X™ Table for Spectrophotometer readings were measured with 1cm path length cuvettes against deionized water and CB-X™ Table for Microplate Reader readings were measured using Nunc™ Immuno 96 MicroWell™ Plates (MaxiSorp™ ) [Cat# 442404] against deionized water.
High sensitivity (low input) miRNA Illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) v6
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 Gram-Negative Bacteria 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 gram-negative bacteria. Please refer to the appropriate protocol depending on your application.
SpinOUT™: Buffer Exchange v1
Authors: not provided G-Biosciences
Published: June 2017

SpinOUT™ protocol for buffer exchangeof peptide and protein samples. (Cat. # 786-170 to 786-173, 786-703 to 786-708, 786-865 to 786-869)
High sensitivity miRNA illumina library preparation protocol by TailorMix miRNA Sample Preparation Kit (Version 2) v2
Authors: Yip Karen , Kelvin Chan not provided , Danny Lee not provided
Published: June 2017

ThI high sensitivity miRNA library generation for the Illumina sequencing platform. Our 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 Cultured Cells 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 cultured cells. Please refer to the appropriate protocol depending on your application.
OmniPrep™ For High Quality Genomic DNA Extraction From Fungal 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 fungal tissue. Please refer to the appropriate protocol depending on your application.
OmniPrep™ For High Quality Genomic DNA Extraction From Blood 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 blood samples (excluding whole blood). Please refer to the appropriate protocol depending on your application.
XIT™ Genomic DNA Blood Kit Protocol for Isolation of Genomic DNA (for 5ml blood) v1
Authors: not provided G-Biosciences
Published: June 2017

This is a protocol forthe Isolation of Genomic DNA from Fresh Blood, Bone Marrow & Buffy Coat (5ml blood). If the buffy coat preparation was processed from 5ml whole blood then follow the Protocol for 5ml Blood. (Cat. # 786‐294, 786‐295, 786‐296)
Flex-T™ Tetramer and Cell Staining Protocol v1
Authors: Miller Kelsey
Published: June 2017

Using UV-induced peptide exchange, MHC/peptide monomers can be generated with conditional Flex-T™ monomers that harbor peptides of interest in their binding grooves. These new MHC monomers are subsequently multimerized using streptavidin-fluorophore conjugates. The resulting Flex-T™ reagents can be used for staining antigen-specific T cells and flow cytometric analysis. In humans, the MHC molecules are called HLA (Human Leukocyte Antigen).
Picking colonies v1
Authors: Hessen-Schmidt Sarah
Published: June 2017

Picking colonies from TCBS Agar plates to 96 well plates for growth
Protocol for STO Cell Transfection by FuGENE HD v1
Authors: Gurevich Misha , V. Katerov not provided
Published: June 2017

Protocol for Transfection Mouse Embryonic Stem Cells.
Protocol for transfection of H4, (ATCC®: HTB-148) Cells by FuGENE HD in 96 well plates. v1
Authors: Gurevich Misha , V. Katerov not provided
Published: June 2017

This is a protocol for transfection of H4 (Human Brain Neuroglioma) in either 10% or 100% FBS using FuGENE HD.
MegaLong™ Protocol for Isolation of >100kb Genomic DNA (Yeast DNA) 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 yeastsamples. Please refer to the appropriate protocol, depending on your application.
A Non-Interfering™ (NI) Protein Assay v1
Authors: not provided G-Biosciences
Published: June 2017

The Non-Interfering™ Protein Assay is a colorimetric assay fordetermining protein concentrations in protein loading buffer (Laemmli buffer), high β-mercaptoethanol concentrations,and in lipid and vesicle preparations.
Buffers for Chloroplast Isolation from Diatoms v1
Authors: Dreux Chappell P. , Bethany D. Jenkins not provided
Published: June 2017

Guide for reagent/buffer preparation for 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.
PCTE filter staining v1
Authors: Stedman Ken
Published: June 2017

For use in "PCTE Protocol for VLP enumeration"
Kane Lab Lyophilized Coffee v1
Authors: Kane Larry
Published: June 2017

This collection is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here. From Larry Kane:Back when I was a tech before grad school, made my own instant coffee by lyophilizing coffee (and drank it) (Image: Instant ! (Explored), Craig Sunter, CC BY-ND)
Isolation from Lysogens v1
Authors: M. Stedman Kenneth , Kate Porter not provided , and Mike L. Dyall-Smith not provided
Published: June 2017

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.
Exotic Lab Methods v1
Authors: scientists Numerous
Published: June 2017

This collection is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More detailshere. If you know creative/unusual protocols like these, please tweet them to #ExoticMethods, e-mail to "info@protocols.io", or share directly as a protocol here, tagging with "ExoticMethods".
Yeast Protein Extraction Sample Buffer v1
Authors: Cone Alan
Published: June 2017

Fresh Protein Extraction Sample Buffer.
Yeast Crude Protein Extraction v1
Authors: Cone Alan
Published: June 2017

Quick crude protein extraction from budding or fission yeast.
VBRC Base By Base: Import genome sequences from Virology.ca viral databases 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: Export a text overview of the alignment 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
Script P4: Assigning Viral Taxonomy v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method for identifying bacteriophage/virus taxonomy without a virome dataset using UniProt reference database. 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."mBio6.5 (2015): e01578-15.
Script R2: Whole Metagenome Contig and Sequencing Statistics v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines 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."mBio6.5 (2015): e01578-15.
Script P10: CRISPR Identification v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocol provides a method for identifing CRIPR repeats using the program PilerCR on assembled contigs. 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.
Charcoal treatment of seawater to remove organics (esp. vitamins). v1
Authors: Paerl Ryan
Published: June 2017

Charcoal treatment of seawater for removal of organics. This is an updated approach to that used by Carlucci & Silbernagiel, 1970. The approach was used in Paerl et al., 2015 Limnology and Oceanography; DOI: 10.1002/lno.10009
Script R8: Plotting Bacterial Taxonomy from MetaPhlan v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the analysis used to plot MetaPhlAn taxonomic assignments. 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.
Generating viral metagenomes from the coral holobiont v1
Authors: D. Weynberg Karen , Elisha M. Wood-Charlson not provided , Curtis A. Suttle not provided , and Madeleine J. H. van Oppen not provided
Published: June 2017

Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis.
Script R14: CARD Antibiotic Resistance Analysis v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines our analysis of the potential antibiotic resistance genes found within the skin virome. We start by visualizing the relative abundances of the top 10 antibiotic resistance categories (according to the CARD). We then quantify the number of unique antibiotic resistance gene categories annotated in the samples at each skin site, and also look at the percent CARD annotated ORFs of the overall ORFs present in each sample at each skin site.
Script R15: CoNet Analysis - Formatting Relative Abundance Files v1
Authors: GD HANNIGAN , GRICE EA not provided , ET AL. not provided
Published: June 2017

This protocoloutlines the analysis used to generate input files for CoNet for the phage-bacteria network. 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.
MECH step CsCl density gradients v1
Authors: D. WEYNBERG KAREN , ELISHA M. WOOD-CHARLSON not provided , CURTIS A. SUTTLE not provided , AND MADELEINE J. H. VAN OPPEN not provided
Published: June 2017

For use in Generating viral metagenomes from the coral holobiont.
TruSeq RNA kit protocol (with one-third reaction volumes and some minor changes) v1
Authors: Jayaprakash Anitha , Jaehee Shim not provided , and Ravi Sachidanandam not provided
Published: June 2017

Version February 14th, 2012
The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome v1
Authors: GD Hannigan , Meisel JS not provided , Tyldsley AS not provided , Zheng Q not provided , Hodkinson BP not provided , SanMiguel AJ not provided , Minot S not provided , Bushman FD not provided , Grice EA not provided
Published: June 2017

This collection contains protocolsfor the computational analysis performed in the paper"The Human Skin dsDNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and its Dynamic Associations with the Host Microbiome".Geoffrey Hannigan and Jacquelyn Meisel are graduate students in Dr. Elizabeth Grice's lab in the Department of Dermatology at the University of Pennsylvania. 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.
PCR amplification of the SISPA primer reaction mixture v1
Authors: D. Weynberg Karen , Elisha M. Wood-Charlson not provided , Curtis A. Suttle not provided , and Madeleine J. H. van Oppen not provided
Published: June 2017

For use in Generating viral metagenomes from the coral holobiont.
PCR amplification of the SISPA primer denaturing cycles v1
Authors: D. WEYNBERG KAREN , ELISHA M. WOOD-CHARLSON not provided , CURTIS A. SUTTLE not provided , AND MADELEINE J. H. VAN OPPEN not provided
Published: June 2017

For use in Generating viral metagenomes from the coral holobiont.
Viral metagenomic analysis on Cabbage Patch Kids v1
Authors: Burnton Stanton
Published: June 2017

This protocol is a parody of an existing scientific journal article and is intended to showcase the features available on the protocols.io platform in order for VERVE Net members to developefuture protocols. While the viral metagenomic analysis on Cabbage Patch Kids is impossible to perform, due to the real-world non-existant nature of Cabbage Patch kids, the sourcedarticle isMetagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal virusesand the "Material and methods" section has been adapted from using actual lettuce data toa metagenomic protocol for Cabbage Patch Kids.
Cracking buffer, 4X (10 mL) v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.
SDS-PAGE Cracking Buffer v1
Authors: Dunigan and Irina Agarkova David
Published: June 2017

Recipe to make 10ml of 2x stock
CviRI Assay Conditions v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
Viral metagenomic analysis on Cabbage Patch Kids v3
Authors: Burnton Stanton , Tiong Gim Aw not provided , Samantha Wengert not provided , Joan B. Rose not provided
Published: June 2017

This protocol is a parody of an existing scientific journal article and is intended to showcase the features available on the protocols.io platform in order for VERVE Net members to developefuture protocols. While the viral metagenomic analysis on Cabbage Patch Kids is impossible to perform, due to the real-world non-existant nature of Cabbage Patch kids, the sourcedarticle isMetagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses written by Tiong Gim Aw, Samantha Wengert, and Joan B. Rose (included in the authors section)and the "Material and methods" section has been adapted from using actual lettuce data toa metagenomic protocol for Cabbage Patch Kids.
CviJI Buffer B, pH 8.5 v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
Extracting DNA from bananas v1
Authors: Wilson Sayres Melissa
Published: June 2017

For more information and for the Spanish version of this protocol, please see here. The protocol is based on:http://www.scientificamerican.com/article/find-the-dna-in-a-banana-bring-science-home/.
CviRI Buffer C v1
Authors: DUNIGAN AND IRINA AGARKOVA DAVID
Published: June 2017

For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.
Transformation of supercompetent cells v1
Authors: Lunt Dave
Published: June 2017

Protocol to prepare E. coli supercompetent cells to transform with plasmid/ligation. This protocol is originally derived from Hanahan, D. (1983) J. Mol. Biol. 166:557-580 with minor changes. This version works exceptionally well for cloning PCR products where the number of colonies is not expected to be as high as from some ligations. These cells outperform commercially purchased supercompetent cells in my hands.
Preparing Data for vContact from Proteins (Cyverse) v1
Authors: Bolduc Benjamin
Published: June 2017

Preparing data for use in vContact by usingVirSorted Ocean Sampling Day (2014) contigs, using tools available inCyverse. 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.
Dimethylglyoxime reagent for cobalt analyses v1
Authors: Bundy Randie
Published: June 2017

This protocol describes how to recrystallizedimethylglyoxime in order to purify it for use in measuring total dissolved and labile cobalt using cathodic stripping voltammetry. This procedure makes a 0.1 mol L-1DMG solution.
Cobalt standard reagent for dissolved cobalt analyses v1
Authors: Bundy Randie
Published: June 2017

This protocol describes how to make a 5 nmol L-1 cobalt standard for measuring dissolved cobalt by cathodic stripping voltammetry.