Protocols

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.

Filter-aided expansion proteomics facilitates spatial proteomics at subcellular resolution by integrating tissue expansion, imaging-guided microdissection and filter-aided in-gel digestion. This combination enhances the resolution, throughput and reproducibility for data-independent acquisition-based mass spectrometry analysis.

Here, the authors provide a platform for inducible CRISPR–Cas9 screening to interrogate non-proliferative cellular states.

Protocol for generating spatially patterned, human neural tube- and forebrain-like structures, by using a microfluidic device to impose orthogonal and independent chemical gradients on human pluripotent stem cells.

The simultaneous recording of fast-scan cyclic voltammetry and functional magnetic resonance imaging signals enable the coupling of local tissue oxygen and neurotransmitter dynamics for measuring changes in the brain

The synthesis of complex carbohydrates requires multiple steps, one of which is 1,2-cis-selective glycosylation. This protocol describes an iron-catalyzed, general approach to formation of rather challenging 1,2-cis-aminoglycosidic linkages.

To understand enzymatic redox reaction mechanisms, it is important to investigate the redox behavior at the metal centers. This Protocol describes metalloenzyme attachment to electrodes and how to perform X-ray absorption spectroelectrochemistry.

Optoelectronic devices based on two-dimensional layered thin film semiconductors can be tuned to directly sense and process spatial and temporal information, making them suitable to use as in-sensor computing devices.

NanoVar is a structural variant caller for low-depth long-read sequencing data, allowing repeat element annotation of non-reference insertion variants. This is a comprehensive guide, from quality assessment of raw data to downstream analysis.

This protocol for imaging-based highly multiplexed in situ profiling of the spatial transcriptome uses three methods: antibody-based protein comapping with STARmap PLUS, ribosome-bound mRNA mapping with RIBOmap and spatiotemporal transcriptome mapping with TEMPOmap.

A technique for ultrasound-induced luminescence imaging, which uses a dual-stage energy conversion mechanism to enhance the performance of luminescence.

In the virus-encoded CRISPR-based direct readout system, single-guide RNA libraries are expressed directly from the genomes of viruses so that single-guide RNA abundance at distinct stages of the viral infection cycle provides direct and quantitative readout of gene-perturbation effects on viral propagation.

Mehl and colleagues present a protocol for selecting aminoacyl-tRNA synthetase (RS)/tRNA pairs from a publicly available MaPylRS active site mutant library for specific and efficient incorporation of noncanonical amino acids into proteins.

Aspiration-assisted bioprinting is a versatile biofabrication technique that enables the precise and selective patterning of biologics, such as tissue spheroids and organoids, addressing the limitations of conventional bioprinting techniques.

This Protocol provides detailed instructions for performing NAP-seq, an RNA sequencing technique for profiling full-length sequences of noncapped RNAs with various terminal modifications at single-nucleotide resolution.

This protocol describes a versatile strategy to generate structurally and functionally programmable hydrogels by using biological membranes as cross-linkers. This enables properties of tissues like muscle and skin to be mimicked.