Research articles

Channel-forming membrane proteins control solute exchange across membranes, and they are difficult to obtain with sufficient yield and purity. This protocol describes a universal approach to their expression (in Escherichia coli), extraction and purification.

An approach that combines a pH-sensitive synaptic biomarker expressed in vivo with the ex vivo staining of oligodendrocyte precursor cells enables quantification of synapse engulfment by oligodendrocyte precursor cells at single-cell and population-level resolution.

MINUTE-ChIP is a multiplexed chromatin immunoprecipitation and sequencing method that measures global and locus-specific changes in histone modification patterns and chromatin factor binding across multiple samples and conditions.

This protocol describes a method for haplotype phasing plant genomes, using gamete cells to enable chromosome-level phasing and crossover detection without the need for Hi-C data or sequencing of large plant populations.

This protocol presents a method for calibrating circular RNA abundance for comparison between RNA sequencing libraries, utilizing a spike-in of synthetic circular RNAs.

This protocol presents a method that combines genome-wide CRISPR libraries with cell coculture in droplets to study functional regulators of cell–cell communication.

Most naturally occurring O-GalNAc glycans can be synthesized from eight glycan core structures. This protocol describes their synthesis from a common precursor via reactions with four glycosyl donors.

In this protocol update, the authors improve on their previous protocol for genome engineering of mammalian cultured cells with CRISPR–Cas9 to generate homozygous knock-ins of fluorescent tags into endogenous genes, to increase both efficiency and throughput.

Feature-based molecular networking is used to analyze non-targeted liquid chromatography–tandem mass spectrometry metabolomics data. This protocol includes instructions, ready-made code and a web app (https://fbmn-statsguide.gnps2.org/) for statistical analysis of feature-based molecular networking results.

Surface tension, interfacial tension and interfacial rheological properties can be calculated from droplet images. This article presents a standardized protocol for pendant-drop tensiometry and the oscillating drop method in two- and three-phase systems.

We present a practical workflow for end-to-end weakly supervised deep learning to predict biomarkers directly from whole-slide images, enabling clinical researchers to work with engineers to set up a complete computational pathology project.

CellChat enables systematic inference, quantitative analysis and intuitive visualization of cell–cell communication from single-cell transcriptomic data, as well as comparative analysis of intercellular communication across biological conditions.

A cost-effective, facile, versatile and ultrafast methodology to fabricate perfusable microchannels of complex shapes in photopolymerizable hydrogels without the need for specialized equipment or sophisticated protocols.

Protocol for the generation of a stem cell-derived human postimplantation embryo model by the combination of embryonic and transgene-induced extraembryonic-like cells.

This protocol covers the production and construction of new-generation transmorphic phage/adeno-associated virus vectors for the systemic delivery of nucleic acid payloads. In vitro and in vivo applications of transmorphic phage/adeno-associated virus particles are also discussed.

This protocol for the precise tracking of nanoparticles in plant roots uses CLSM for macroscopic tissue examination and TEM for cellular-level analysis and provides methodologies for preparing plant materials before imaging.

DiMeLo-seq uses long-read, single-molecule sequencing to map protein–DNA interactions genome wide. This allows mapping of multiple interaction sites on single DNA molecules and profiling protein binding in the context of endogenous DNA methylation.

The three methods present visualize epigenetic modifications and their spatial proximities in single cells; base-encoded amplifying FISH, pairwise proximity-differentiated amplifying FISH and cellular macromolecules-tethered DNA walking indexing.

This protocol extension details two approaches to creating a bioswitchable delivery system for microRNA therapeutics, based on a tetrahedral DNA nanostructure with a ribonuclease H-sensitive sequence as a bioswitchable apparatus for the controlled release of cargo.

High-resolution diffusion uses a dense optical flow algorithm to quantify and classify the motion of nuclear macromolecules, assigning biophysical parameters such as the diffusion constant, the anomalous exponent and the drift velocity.