Protocols

This protocol presents a versatile, easy-to-apply procedure for fabricating high-resolution cell-adhesive micropatterns, offering an affordable and scalable solution amenable to non-specialist cell biology teams.

High-speed atomic force microscopy (AFM) provides submolecular resolution topographic information to improve our understanding of protein dynamics. This protocol describes how to prepare suitable AFM tips via focused electron beam–induced deposition using a benchtop scanning electron microscope (SEM).

MRIQC is software designed to help researchers assess the quality of reconstructed MRI scans before they undergo further data analysis. This protocol provides advice on how to use MRIQC for visual assessment of example artifacts.

We present a detailed protocol for the building and testing of an isoSTED nanoscopy setup that enables the 3D imaging of biological samples with isotropic sub-50-nm resolution at ≤35 µm in depth.

The design of optically transparent ultrasound transducers facilitates the building of compact biomedical instruments for the concurrent combination of optical and ultrasound-based stimulation and imaging in experimental workflows.

Nanomaterials acquire a dynamic corona of adsorbed proteins when exposed to biological fluids. This protocol enables the identification of these corona proteins, the quantification of their dynamics, and the mapping of receptor–corona interactions.

This protocol describes a modular method to perform high-throughput electrophysiology on human induced pluripotent stem cell-derived cardiomyocytes, through a combination of simultaneous population patch-clamp and robotic liquid handling.

This protocol presents IPOD-HR, a high-resolution approach for profiling genome-wide protein occupancy in bacteria, supported by a computational pipeline for streamlined downstream analysis.

Nucleoside analogs are used in the treatment of diseases and as components of oligonucleotide therapeutics. This protocol describes a generalized, five-stage synthesis of C4′-modified nucleoside analogs (10 C4′ modifications and 20 nucleobases).

The wildDISCO protocol is used for whole-body immunolabeling, optical clearing and imaging of mice at cellular resolution using standard IgG antibodies.

This protocol forms large, reversibly gated membrane channels by coupling nanoscale reconfiguration of DNA origami rafts to microscale deformation and recovery of giant unilamellar vesicles, allowing spatiotemporal regulation of compartmentalized biochemical reactions and functional engineering of synthetic cells.

Geneformer is a foundational model that enables mapping interactions between genes within networks. The trained model can then be applied to predict the effect of gene perturbations on cell states in settings with limited data.

This Protocol describes a statistical tool for differential protein expression analysis in quantitative mass spectrometry-based proteomics (DEqMS). It can be applied to both data-dependent and data-independent acquisition workflows.

The peptide-centric local stability assay (PELSA) is used to identify ligand targets and binding regions at the proteome scale. By subjecting native proteins to brief yet extensive trypsin digestion, this method generates local stability profiles.

The modulation of illumination patterns within a 3D volume enables the rapid photopolymerization of protein-based (bio)ink for volumetric bioprinting, with the highest resolution in the sub-50-μm range.

Quantum dots are used in many display and imaging applications. Preparing blue quantum dots that are heavy-metal-free has been challenging. This Protocol describes the tunable synthesis of ZnSeTeS quantum dots with narrow emission bands in the violet–blue range.

The trRosettaRNA server is a web-based platform for automated and accurate RNA 3D structure prediction using deep learning. This protocol also describes how to use the standalone package locally, which is beneficial for large-scale applications.

This Protocol describes an automated approach for optical labeling of therapeutic monoclonal antibodies by using disposable commercial components, yielding a cGMP-grade product at reduced cost and without the need for a dedicated clean room facility.

This protocol uses Reprogrammable Adenosine Deaminase Acting on RNA (ADAR) Sensors (RADARS) to robustly sense RNA transcripts inside eukaryotic cells, enabling detection of changes in gene expression or targeting and perturbation of specific mammalian cell types and states.

This Protocol describes the transcriptome-wide labeling of RNAs in a particular subcellular compartment using proximity biotinylation by localized APEX2 enzyme and subsequent enrichment and sequencing of these transcripts.