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Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing
10.1038/nprot.2017.150 2018-02-22 G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer ... |
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Generation of human brain region–specific organoids using a miniaturized spinning bioreactor
10.1038/nprot.2017.152 2018-02-22 Human brain organoids, 3D self-assembled neural tissues derived from pluripotent stem cells, are important tools for studying human brain development and related disorders. Suspension cultures maintained by spinning bioreactors allow for the growth of large o... |
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Monitoring intracellular nanomolar calcium using fluorescence lifetime imaging
10.1038/nprot.2017.154 2018-02-22 Nanomolar-range fluctuations of intracellular [Ca2+] are critical for brain cell function but remain difficult to measure. We have advanced a microscopy technique to monitor intracellular [Ca2+] in individual cells in acute brain slices (also applicable in vi... |
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Production of ready-to-use few-layer graphene in aqueous suspensions
10.1038/nprot.2017.142 2018-02-15 Graphene has promising physical and chemical properties such as high strength and flexibility, coupled with high electrical and thermal conductivities. It is therefore being incorporated into polymer-based composites for use in electronics and photonics appli... |
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An experimental toolbox for characterization of mammalian collagen type I in biological specimens
10.1038/nprot.2017.117 2018-02-15 Collagen type I is the most abundant extracellular matrix protein, and collagen type I supramolecular assemblies (e.g., tissue grafts, biomaterials and cell-assembled systems) are used extensively in tissue engineering and regenerative medicine. Many studies,... |
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Proteome-wide identification of ubiquitin interactions using UbIA-MS
10.1038/nprot.2017.147 2018-02-15 Ubiquitin-binding proteins play an important role in eukaryotes by translating differently linked polyubiquitin chains into proper cellular responses. Current knowledge about ubiquitin-binding proteins and ubiquitin linkage-selective interactions is mostly ba... |
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Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C
10.1038/nprot.2017.132 2018-02-08 Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, int... |
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Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data
10.1038/nprot.2017.146 2018-02-08 This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are c... |
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Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins
10.1038/nprot.2017.145 2018-02-01 This protocol is an extension to:Nat. Protoc. 9, 2395–2410 (2014); doi:10.1038/nprot.2014.157; published online 18 September 2014 |
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Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins
10.1038/nprot.2017.113 2018-02-01 Cross-linking coupled with mass spectrometry (XL-MS) has emerged as a powerful strategy for the identification of protein–protein interactions, characterization of interaction regions, and obtainment of structural information on proteins and protein complexes... |