Research articles

This protocol combines pooled CRISPR–Cas9 screening with neural organoid and assembloid models and illustrates how it can be applied to map hundreds of disease genes onto cellular pathways and specific aspects of human neural development.

Virus infection real-time imaging visualizes viral RNA translation within cells in real-time, revealing the earliest events of viral infection when viral protein and RNA levels are low, as well as the origins and consequences of cell-to-cell heterogeneity during virus infection.

Deformable poly-acrylamide co-acrylic acid microparticles (DAAM-particles) are tunable hydrogel microparticles for quantifying cellular forces. This comprehensive protocol details their synthesis, functionalization and applications.

This protocol integrates state-of-the-art microfabrication, tissue engineering and optogenetic approaches to generate topobiologically complex miniature colons capable of undergoing tumorigenesis in vitro.

Rigorous characterization is important for developing electrocatalytic reactions, for example, nitrate reduction. This workflow integrates bulk and surface techniques with in situ/operando spectroscopies, electrochemical measurements and density functional theory calculations.

The Mant-ATP assay is a simple and accessible means for rapid quantitative assessment of the ratio of super-relaxed myosin to disordered relaxed myosin. This protocol provides a standardized methodology to perform the assay across a range of systems.

This Protocol describes XomicsToModel, a semi-automated pipeline that integrates bibliomic, transcriptomic, proteomic and metabolomic data with a generic genome-scale metabolic reconstruction or model.

The authors present a protocol for the use of two advanced DNA-based tension probes, the reversible shearing DNA-based tension probe (RSDTP) and ForceChrono probe, which provide powerful tools for studying mechanotransduction in living cells.

This Protocol Extension describes directional conjugation of monoclonal antibodies to nanoparticles via the Fc antibody moiety using metal-free click chemistry, including procedures for synthesis, quality control and evaluation of nanoparticle–antibody conjugates.

This protocol for the use and quality control of genetically encoded reporters to label proteins and cells in correlative light and electron microscopy workflows enables the acquisition of molecular, cellular and biochemical information at high resolution.

This robust, proteome-wide approach for the exploration of the S-nitrosoproteome in human and mouse tissues uses the SNOTRAP probe and nano-liquid chromatography–tandem mass spectrometry analysis. The protocol enables efficient and high-throughput profiling of S-nitrosylated proteins in complex mixtures of biological material.

BreakTag is a scalable next-generation sequencing-based method for the unbiased characterization of programmable nucleases and guide RNAs that allows off-target and nuclease activity assessment, as well as the characterization of scission profiles.

Reproducible characterization of materials designed for radiative cooling is important for their development and application. The protocol describes how to acquire optical data and how to build and use outdoor and indoor thermal testing platforms.

This Protocol describes preprocessing of different environmental samples and extraction of microplastics and nanoplastics, as well as qualitative and quantitative characterization of microplastics and nanoplastics. The analytical technologies used for characterization include attenuated total reflection-Fourier transform infrared spectroscopy, laser direct infrared spectroscopy and optical photothermal infrared microspectroscopy.

This protocol describes the synthesis of macrocyclic macroPROTAC1 and trivalent PROTAC SIM1, detailing the generation of the macrocyclic and trivalent cores and their conjugation to the respective ligands, for enhanced target protein degradation.

We provide a protocol for generating human pluripotent stem cell-derived blood-generating heart-forming organoids, a multitissue model encompassing aspects of human cardiac, endothelial and hematopoietic co-development, and techniques to stain and clear these large samples for laser microscopy.

ANPELA is a software package to compare and assess the performance of different workflows for processing single-cell proteomic data, ensuring the user selects the most appropriate processing workflow for their experimental design question.

The preparation of multicomponent viscoelastic self-enhancing sono-inks, synthesized as phase-transition reversible acoustic absorbers, enables acoustic volumetric printing beneath diverse tissue types in optically scattering media.

In mass photometry, the optical contrast generated by individual molecules at a glass–water interface enables mass-resolved quantification of biomolecular mixtures. This protocol describes how to optimize and validate this method.

Protocol for fabricating synthetic viscoelastic antigen-presenting cells and their application in T cell engineering. These synthetic cells support robust T cell activation and expansion and improve chimeric antigen receptor transduction efficiency.