In this Protocol Extension, the authors extend their original Protocol used to generate a genome-scale metabolic model for a single strain to enable multi-strain models to be made, which can be used to study pan-metabolic capabilities and strain-specific differences across a species.

Tumor-reactive T cells are generated by coculturing tumor organoids and autologous peripheral blood lymphocytes and are evaluated for their capacity to carry out effector functions after recognition of tumor cells and whether they kill tumor organoids.

Bacterial extracellular vesicles (BEVs) in human body fluids are analyzed using ultrafiltration, size-exclusion chromatography and density-gradient centrifugation to separate the BEVs, followed by post-separation characterization with orthogonal biochemical methods.

Single-cell micrococcal nuclease sequencing (scMNase-seq) profiles nucleosome positions and chromatin accessibility genome-wide in single cells.

DNA has the capacity to store large amounts of information for very long durations. This protocol describes encoding of digital files as DNA and the error-free retrieval of the stored data from the sequenced data.

This protocol describes a collection of pH-sensitive fluorescent reporters that can be used for real-time dual-color imaging of exosome release from single cells. The authors provide detailed instructions for TIRF imaging and automated data analysis.

This Protocol describes a low-cost and scalable solid-state nanopore fabrication method, termed controlled breakdown (CBD), for fabricating solid-state nanopores.

G protein–coupled receptors (GPCRs) play a central role in physiological processes and are common drug targets. This GPCR precrystallization screen uses small culture volumes to determine which conditions result in maximal protein expression and stability.

This protocol describes a mass spectrometry–based workflow for combined analysis of protein phosporylation and N-glycosylation of extracellular vesicles obtained from a single blood plasma sample.