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Nature Protocols



Nature Protocols is an interactive online resource for laboratory protocols for bench researchers. The core content is high quality, peer-reviewed protocols that are presented in a 'recipe' style, providing step-by-step descriptions of procedures that use



 



Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins

2018-02-01

This protocol extension describes DNA-free genome editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. The authors' previously published protocol for genome editing of wheat used CRISPR/Cas9 plasmids.



Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins

2018-02-01

This protocol describes a cross-linking mass spectrometry (XL-MS) approach to studying homodimer interfaces, and provides procedures for stable isotope–labeling of one of the two monomers, homodimer refolding, XL-MS, and data analysis.



Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C

2018-02-08

This protocol describes targeted chromatin capture (T2C), a high-resolution method to interrogate 3D chromatin organization and genomic interactions at sub-kilobase-pair resolution that requires minimal cell numbers and sequencing depth.



Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data

2018-02-08

This protocol describes how to use distance restraints obtained from cross-linking mass spectrometry (XL-MS) experiments to guide the structural prediction of proteins and protein complexes.



Production of ready-to-use few-layer graphene in aqueous suspensions

2018-02-15

Graphene has a unique set of extraordinary mechanical, optical, and electronic properties, but is difficult to prepare in large amounts. This protocol describes how to prepare three- to four-layer-thick graphene in stable water suspensions and powder form.



An experimental toolbox for characterization of mammalian collagen type I in biological specimens

2018-02-15

This protocol describes a set of assays for characterization of the quality and quantity of mammalian collagen type I from a diverse range of biological samples.



Proteome-wide identification of ubiquitin interactions using UbIA-MS

2018-02-15

This protocol describes the chemical synthesis of different nonhydrolyzable diubiquitin linkages and their use in affinity purification and LC–MS/MS identification of linkage-selective diubiquitin interactors.



Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

2018-02-22

This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific single-chain antibody. This enables the determination of G4 structure formation genome-wide in chromatin.



Generation of human brain region–specific organoids using a miniaturized spinning bioreactor

2018-02-22

This protocol describes procedures for building the SpinΩ bioreactor for 3D tissue culture and differentiating human iPSCs into different brain region–specific organoids resembling developing human dorsal forebrain, midbrain and hypothalamus.



Monitoring intracellular nanomolar calcium using fluorescence lifetime imaging

2018-02-22

This protocol describes an improved fluorescence lifetime imaging (FLIM) approach for nanomolar calcium imaging using the OGB-1 fluorescent calcium indicator in brain cells in situ.