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V2a interneurons are differentiated from mouse and human pluripotent stem cells following culture in the presence of a sequence of small-molecule treatments.
tRNA modifications are important for normal and disease states, but methods to study them are lacking. This protocol relies on chemical cleavage at 7-methylguanosine (m7G) sites, followed by sequencing, to precisely map these modifications genome-wide.
iMARGI (in situ mapping of RNA–genome interactome) is a proximity ligation method for global profiling of chromatin-associated RNAs. A linker sequence bridges DNA and RNA in physical proximity, permitting sequencing library preparation and mapping of DNA–RNA contacts.
This protocol combines hydrogen–deuterium exchange mass spectrometry (HDX-MS) of membrane proteins in nanodiscs with molecular dynamics (MD) simulations to identify lipid–protein interactions that modulate conformational changes.
Fusing the SNAP-tag to a disease-specific protein of interest allows its directed functionalization with a synthetic benzylguanine-modified diagnostic or therapeutic label in a 1:1 stoichiometry. This protocol describes how to produce, conjugate and test the activity of the corresponding combination products.
This protocol describes SpiderMass, a platform for in vivo and real-time mass spectrometry analysis. The procedure describes system setup and calibration; analysis of cell culture, tissue section and in vivo skin samples; and data processing.
Microvessels are isolated from mouse brain cortex, minimizing cell activation and yielding microvessel fragments with consistent populations of discrete blood–brain barrier components that retain RNA integrity and protein post-translational modifications.
Self-organizing 3D human blood vessel organoids are generated by mesoderm induction of hPSC aggregates and subsequent differentiation into endothelial networks and pericytes in a 3D collagen I–Matrigel matrix.
BACMMAN software is used to automate image analysis of high-throughput 2D or 3D time-series images from experiments using the ‘mother machine’, a microfluidic device that allows growth and division of single bacterial cells to be followed.
This protocol uses a microfluidic device and microscopy to detect mutations occurring as a consequence of DNA replication and assess their effects on fitness in Escherichia coli single cells.
Specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) allows multiplexed, portable, and ultra-sensitive detection of RNA or DNA from clinically relevant samples.
These rhodium-catalyzed asymmetric Suzuki–Miyaura reactions couple racemic allyl halide starting materials with sp2-hybridized boronic acid derivatives to provide access to enantiomerically enriched cyclic allylic products.
This protocol provides guidelines for designing and validating antibody panels for fluorescence-based imaging of FFPE tissue sections using cyclic immunofluorescence (t-CyCIF) or other multiplexed imaging methods.
This protocol enables gene delivery in intact plants using high-aspect-ratio carbon nanotubes (CNTs). The procedure contains detailed instructions for the functionalization of CNTs, DNA loading, delivery, and transgene expression characterization.
This protocol describes the synthesis, purification, functionalization and characterization of nitrogen-doped carbon nanodots (NCNDs). In addition, examples of how to tailor the color emission, electrochemistry and chirality of NCNDs are provided.
This computational protocol functionally links bacterial or archaeal genes within a dataset, enabling reliable functional predictions to be extracted for uncharacterized genes. As one example, the authors describe the ‘CRISPRicity’ metric to link genes to CRISPR–Cas systems.
This protocol describes the detailed procedures for design, assembly, and characterization of different types of double-stranded DNA nanostructures, as well as a number of downstream applications.
The production of nanomaterials has increased, but their environmental impact is uncertain. This protocol describes stable isotope labeling of metal and metal oxide nanomaterials to enable tracing in aquatic and terrestrial environments and within organisms.
Cardiac tissues are derived from hiPS cells and electromechanically matured toward an adult-like phenotype. This protocol also describes optimized methods for analyses of function, ultrastructure, and cellular properties of these tissues.
Precise quantification of metabolic pathway fluxes is needed in many applications, e.g., microbiological engineering. The authors describe a GC–MS method for 13C metabolic flux analysis with data analysis using Metran software.