This protocol describes a method for isolating extracellular vesicles from biofluids or cell culture medium using a chemical probe-based array, including details for constructing the array and characterization and relative quantification of extracellular vesicle proteins using immunoblotting.

Kallisto, bustools and kb-python are a set of tools for quantifying bulk, single-cell and single-nucleus RNA-seq. Together, this set of free, open-source software tools can produce gene expression quantification from raw sequencing reads.

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.

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.

This protocol presents a method for pooled CRISPR perturbation screens to study the intoxication mechanism of bacterial toxins.

This protocol repurposes an Illumina NovaSeq 6000 S4 flow cell for low-cost, submicrometer-resolution spatial transcriptome profiling of a tissue section and provides a comprehensive computational analysis pipeline.

A protocol for common variants of outcome devaluation tasks facilitates standardization of testing goal-directed behavior in rats by detailing control conditions, outcome pre-exposure, habituation to pre-feeding chambers and hunger levels in rats.

This targeted mass spectrometry protocol uses stable isotope-labeled peptides as internal standards for accurate, sensitive identification and quantification of peptides bound to MHCs, nominating potential targets for vaccines and immunotherapies.

Salt stress in plants is an adverse environmental condition that affects agricultural productivity. This protocol describes the synthesis of Aza-CyBz and applications of this NaCl probe to monitoring plant salt stress in Arabidopsis thaliana.

This protocol describes a method for isolating extracellular vesicles from biofluids or cell culture medium using a chemical probe-based array, including details for constructing the array and characterization and relative quantification of extracellular vesicle proteins using immunoblotting.

This protocol covers the surgical ablation of muscle tissue in mice, as a reproducible model of volumetric muscle loss, and the implantation of therapeutic bioscaffolds to induce myogenesis and angiogenesis.

This protocol uses the liquid glycan array (LiGA) platform, a library of DNA-barcoded bacteriophages displaying 5–1,500 copies of a glycan, to allow profiling of glycan–glycan-binding protein interactions on the surface of live cells.

We describe the use of ColabFold to perform structure prediction of monomers, complexes and alternative conformations, either on the web or locally, and provide guidance on interpreting the results through confidence metrics and visualizations.