At Nature Protocols, we aim to publish protocols for the best approaches to techniques from leading experts in each field. All of our protocols have been proven to work already and used to generate data published in a supporting primary research paper. Protocols are externally peer-reviewed and edited in-house to the highest standards. Each protocol contains a full list of reagents and equipment, timing information, and step-by-step instructions for performing the experiment, as well as information on designing and adapting the technique, its advantages and limitations compared to alternatives, troubleshooting, analysing data, and interpreting results. We also encourage authors to submit videos for steps that are technically challenging.
Scope
Nature Protocols aims to publish the protocols being used to answer outstanding biological and biomedical science research questions, including methods grounded in physics and chemistry that have a practical application to the study of biological problems. As the main audience for Nature Protocols articles is research scientists, we only publish protocols that have research applications; thus, we do not publish protocols where the main application is to make decisions that influence patient management and treatment. Specific techniques of interest include, but are not limited to, protocols relating to:
Biochemistry: Enzymology, binding assays, surface-plasmon based resonance, molecular structure determination, analytical ultracentrifugation, UV-visible spectroscopy, IR and NMR, probe scanning, kinetics and thermodynamics, enzyme assays
Cell biology: Apoptosis, cell cycle, senescence, FRET, organelle isolation, migration assays, transport/localization
Cell culture: Isolation and identification, manipulation, transfection, cell equivalents to animal models, primary cell culture, stem cells
Chemical modification: Chemical tagging of biomolecules, labeling, fluorescent labeling, radiolabeling, stable-isotope labeling, chemical ligation, biopolymer synthesis using non-natural monomers, detection of post-translational modifications (phosphorylation, sulfonylation, glycosylation, lipidation, etc), epitope tagging
Computational biology: Management and analysis of sequence data, intron/exon structure identification, expression pattern databases and statistical methods/computer programs to analyze microarrays, protein folding/unfolding analysis, network systems/systems biology and complexity, molecular modeling, quantitative structure-activity relationships, neuroinformatics, phylogenetics, statistics
Developmental biology: Apoptosis, cell cycle, senescence, wound healing assays, fate mapping, cell ablation studies, cell transplantation, transport/localization
Epigenomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, next generation sequencing technology
Genetic analysis: RNAi, mutagenesis, physical mapping, recombination mapping, genetic screens, pedigree analysis, association studies, genotyping, sequencing, arrays, genomics, FISH, promoter and/or enhancer studies, gene expression, splicing, nucleic acid transport, nucleic acid localization, phylogenetics, evo-devo, cytogenetics, molecular diagnostics
Genetic modification: Gene targeting, transduction, RNAi, mutagenesis, bacteriophages, plasmids, transfection, transformation, transgenic manipulation, retroviruses
Genomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, next generation sequencing technology
Imaging: Microscopy, optical spectroscopy, x-ray computed tomography, electron microscopy (including cryo-EM), live cell and tissue imaging, MRI, PET, SPECT, chemical imaging reagents and fMRI, (in vivo) fluorescence and bioluminescence imaging, single molecule techniques
Immunology: Production of antibodies, antibody-based assays, immunolabeling, antibody engineering and xenotransplantation
Isolation, purification and separation: Cytometry, electrophoresis, centrifugation, organelle isolation, chromatography, chiral separation, immunoaffinity, preparation of stationary phases, affinity chromatography, and other separation techniques
Lipidomics: High throughput analysis, microarrays, single molecule detection and characterization
Metabolomics: High throughput analysis, microarrays, mass spectrometry, single molecule detection and characterization
Microbiology: Biofilms, culture, transfection, environmental microbiology, biochemistry, disease models, ecology, evolution and biodiversity, genetics and genomics, genetic modification, metagenomics, pathogenesis and host defense, diagnostics, antimicrobial therapies and vaccines, diagnostic techniques
Model organisms: Yeast, zebrafish, C. elegans, Drosophila, mouse, rat, guinea pig, human, Xenopus, Arabidopsis and others
Nanotechnology: Nanobiology, nanobiotechnology, quantum dots, nanomedicine, drug delivery, imaging contrast agents, nanoelectromechanical devices and lab-on-a-chip technologies
Neuroscience: Electrophysiology, behavioral assays, functional imaging, neuroinformatics, neuronal culture
Nucleic-acid based molecular biology: Libraries and screening, recombinant technology, cloning, PCR-based techniques (including qPCR and RT-PCR), northern, Southern, single molecule detection and characterization, mutation detection, DNA sequencing, hybridization techniques, oligonucleotide sequencing, nucleic acid isolation and purification
Pharmacology: Ligand and small molecule design, receptor binding, surface-plasmon based resonance, high-throughput assays, enzyme assays (including ELISA), ion channel assays, functional assays, chemical genetics/chemical genomics, analysis of drug metabolites and target identification, quantitative structure-activity relationships, animal models
Plant biology: Genetic modification, gene expression, photosynthesis, carbohydrate metabolism, phytohormones, microscopy
Protein analysis: Protein structures, protein interactions, protein engineering, sequencing, BRET, FRET, two-hybrid, three-hybrid, epitope tagging, ion channel assays, other functional assays, detection of post-translational modifications (phosphorylation, sulfonylation, glycosylation, lipidation, etc), coimmunoprecipitation
Proteomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, protein evolution and activity-based proteomics
Spectroscopy: NMR, mass spectrometry, FT infrared spectroscopy, dynamic light scattering, MALDI-TOF, surface-plasmon based resonance spectroscopy, circular dichroism spectroscopy, Raman spectroscopy, EPR (or ESR) spectroscopy
Structural biology: Crystallization, X-ray crystallography, NMR, mass spectrometry, atomic force microscopy, electron microscopy (including cryo-EM)
Synthetic chemistry: Synthesis of unnatural amino acids and peptides, synthesis of natural products and of their precursors, synthesis of catalysts, synthesis of bio-active compounds, reagent synthesis, synthesis of probes for small molecules, named chemical reactions, combinatorial approaches, general synthetic methods (Addition, amination, elimination, enzymatic, epoxidation, hydrogenation, hydroxylation, insertion, metathesis, oxidation, oxidative addition, photochemical, polymerization, radical, reduction, reductive elimination, substitution, thermal, transition metal catalyzed)
Tissue culture: Isolation and identification, manipulation, transfection, tissue equivalents to animal models, tissue engineering and stem cells
Toxicology: Management and analysis of data, predictive ADMETox, receptor binding, surface-plasmon based resonance, high-throughput assays, enzyme assays (including ELISA), ion channel assays, functional assays, chemical genetics/chemical genomics, target identification, quantitative structure-activity relationships, teratology
Virology: Culture, biochemistry, disease models, ecology, evolution, genetics and genomics, genetic modification, metagenomics, pathogenesis and host defense, diagnostics, vaccines, serotyping
Chief Editor: Melanie Clyne
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Scope
Nature Protocols aims to publish the protocols being used to answer outstanding biological and biomedical science research questions, including methods grounded in physics and chemistry that have a practical application to the study of biological problems. As the main audience for Nature Protocols articles is research scientists, we only publish protocols that have research applications; thus, we do not publish protocols where the main application is to make decisions that influence patient management and treatment. Specific techniques of interest include, but are not limited to, protocols relating to:
Biochemistry: Enzymology, binding assays, surface-plasmon based resonance, molecular structure determination, analytical ultracentrifugation, UV-visible spectroscopy, IR and NMR, probe scanning, kinetics and thermodynamics, enzyme assays
Cell biology: Apoptosis, cell cycle, senescence, FRET, organelle isolation, migration assays, transport/localization
Cell culture: Isolation and identification, manipulation, transfection, cell equivalents to animal models, primary cell culture, stem cells
Chemical modification: Chemical tagging of biomolecules, labeling, fluorescent labeling, radiolabeling, stable-isotope labeling, chemical ligation, biopolymer synthesis using non-natural monomers, detection of post-translational modifications (phosphorylation, sulfonylation, glycosylation, lipidation, etc), epitope tagging
Computational biology: Management and analysis of sequence data, intron/exon structure identification, expression pattern databases and statistical methods/computer programs to analyze microarrays, protein folding/unfolding analysis, network systems/systems biology and complexity, molecular modeling, quantitative structure-activity relationships, neuroinformatics, phylogenetics, statistics
Developmental biology: Apoptosis, cell cycle, senescence, wound healing assays, fate mapping, cell ablation studies, cell transplantation, transport/localization
Epigenomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, next generation sequencing technology
Genetic analysis: RNAi, mutagenesis, physical mapping, recombination mapping, genetic screens, pedigree analysis, association studies, genotyping, sequencing, arrays, genomics, FISH, promoter and/or enhancer studies, gene expression, splicing, nucleic acid transport, nucleic acid localization, phylogenetics, evo-devo, cytogenetics, molecular diagnostics
Genetic modification: Gene targeting, transduction, RNAi, mutagenesis, bacteriophages, plasmids, transfection, transformation, transgenic manipulation, retroviruses
Genomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, next generation sequencing technology
Imaging: Microscopy, optical spectroscopy, x-ray computed tomography, electron microscopy (including cryo-EM), live cell and tissue imaging, MRI, PET, SPECT, chemical imaging reagents and fMRI, (in vivo) fluorescence and bioluminescence imaging, single molecule techniques
Immunology: Production of antibodies, antibody-based assays, immunolabeling, antibody engineering and xenotransplantation
Isolation, purification and separation: Cytometry, electrophoresis, centrifugation, organelle isolation, chromatography, chiral separation, immunoaffinity, preparation of stationary phases, affinity chromatography, and other separation techniques
Lipidomics: High throughput analysis, microarrays, single molecule detection and characterization
Metabolomics: High throughput analysis, microarrays, mass spectrometry, single molecule detection and characterization
Microbiology: Biofilms, culture, transfection, environmental microbiology, biochemistry, disease models, ecology, evolution and biodiversity, genetics and genomics, genetic modification, metagenomics, pathogenesis and host defense, diagnostics, antimicrobial therapies and vaccines, diagnostic techniques
Model organisms: Yeast, zebrafish, C. elegans, Drosophila, mouse, rat, guinea pig, human, Xenopus, Arabidopsis and others
Nanotechnology: Nanobiology, nanobiotechnology, quantum dots, nanomedicine, drug delivery, imaging contrast agents, nanoelectromechanical devices and lab-on-a-chip technologies
Neuroscience: Electrophysiology, behavioral assays, functional imaging, neuroinformatics, neuronal culture
Nucleic-acid based molecular biology: Libraries and screening, recombinant technology, cloning, PCR-based techniques (including qPCR and RT-PCR), northern, Southern, single molecule detection and characterization, mutation detection, DNA sequencing, hybridization techniques, oligonucleotide sequencing, nucleic acid isolation and purification
Pharmacology: Ligand and small molecule design, receptor binding, surface-plasmon based resonance, high-throughput assays, enzyme assays (including ELISA), ion channel assays, functional assays, chemical genetics/chemical genomics, analysis of drug metabolites and target identification, quantitative structure-activity relationships, animal models
Plant biology: Genetic modification, gene expression, photosynthesis, carbohydrate metabolism, phytohormones, microscopy
Protein analysis: Protein structures, protein interactions, protein engineering, sequencing, BRET, FRET, two-hybrid, three-hybrid, epitope tagging, ion channel assays, other functional assays, detection of post-translational modifications (phosphorylation, sulfonylation, glycosylation, lipidation, etc), coimmunoprecipitation
Proteomics: High throughput analysis, microarrays, aptamer selection, SAGE, SELEX, single molecule detection and characterization, protein evolution and activity-based proteomics
Spectroscopy: NMR, mass spectrometry, FT infrared spectroscopy, dynamic light scattering, MALDI-TOF, surface-plasmon based resonance spectroscopy, circular dichroism spectroscopy, Raman spectroscopy, EPR (or ESR) spectroscopy
Structural biology: Crystallization, X-ray crystallography, NMR, mass spectrometry, atomic force microscopy, electron microscopy (including cryo-EM)
Synthetic chemistry: Synthesis of unnatural amino acids and peptides, synthesis of natural products and of their precursors, synthesis of catalysts, synthesis of bio-active compounds, reagent synthesis, synthesis of probes for small molecules, named chemical reactions, combinatorial approaches, general synthetic methods (Addition, amination, elimination, enzymatic, epoxidation, hydrogenation, hydroxylation, insertion, metathesis, oxidation, oxidative addition, photochemical, polymerization, radical, reduction, reductive elimination, substitution, thermal, transition metal catalyzed)
Tissue culture: Isolation and identification, manipulation, transfection, tissue equivalents to animal models, tissue engineering and stem cells
Toxicology: Management and analysis of data, predictive ADMETox, receptor binding, surface-plasmon based resonance, high-throughput assays, enzyme assays (including ELISA), ion channel assays, functional assays, chemical genetics/chemical genomics, target identification, quantitative structure-activity relationships, teratology
Virology: Culture, biochemistry, disease models, ecology, evolution, genetics and genomics, genetic modification, metagenomics, pathogenesis and host defense, diagnostics, vaccines, serotyping
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