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Multispectral large-scale single-cell resolution 3D imaging allows up to eight fluorophores to be captured in a single acquisition. This protocol enables the visualization and exploration of large intact tissue volumes.
The authors provide a guide to using the Kraken suite for metagenomics analysis, including classification, quantification and visualization, illustrated by quantification of species in the microbiome and identification of pathogens in a clinical sample.
This two-stage bioreactor-mediated approach for culturing previously uncultured microorganisms involves enrichment of indigenous organisms by using a continuous-flow down-flow hanging sponge bioreactor and subsequent selective batch cultivation.
Little is known about the brain mechanisms of hallucinations. This protocol describes the use of a robotic device and sensorimotor method to reproducibly induce and measure presence hallucinations by behavioral assay and fMRI.
Direct carbonization of zeolitic imidazolate framework-type metal-organic frameworks, as described in this protocol, results in nanoporous carbons that can be used for diverse electrochemical applications.
The cell membrane turnover kinetics of the main glial glutamate transporter GLT1 are quantified by fusing it to a pH-sensitive fluorescent protein and performing measurements using whole-cell fluorescence recovery after photobleaching.
Photochemical methods are increasingly being used in chemical synthesis. This protocol describes how to optimize the reaction conditions for a standard chiral example using cyclodextrin derivatives as supramolecular hosts.
This protocol provides a step-by-step guide to building an affordable single-molecule localization microscopy setup for high-throughput super-resolution imaging by using off-the-shelf and machined parts.
This protocol includes a suite of procedures for measuring the passive permeability of solutes through membranes using fluorescence-based assays that report either volume or pH changes of synthetic vesicles or live cells.
Identifying metabolites in cells of the tumor microenvironment is an area of intense study. This protocol describes specimen collection, enrichment of human immune cell populations and analysis by flow cytometry and LC–MS.
Small-animal blood exchange replaces or dilutes blood components more precisely than parabiosis does. This protocol describes the exchange process, provides blueprints of the required device and derives equations for simulating dilution of biomolecules.
Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. This protocol describes how to build these from computed DFT data and use them to predict and rationalize the performance of homogeneous catalysts.
This protocol uses signaling networks and molecular markers recently elucidated from single-cell transcriptomic analysis of mouse foregut organogenesis to differentiate human pluripotent stem cells into digestive and respiratory organ-specific mesenchyme.
Contamination of water by oil is a problem both in the environment and in engineering applications. This protocol describes how to prepare a transparent superoleophobic film that can coat lenses or make separation membranes for use underwater.
This protocol describes the isolation from brain tissue of extracellular vesicle subpopulations, including microvesicles, exosomes and mitochondria-derived mitovesicles, using a high-resolution (iodixanol) density step gradient. Extracellular vesicle characterization and analysis are also presented.
This protocol describes prime editing (PE) and twinPE experiments as well as the design and optimization of pegRNAs. The authors provide guidelines for selecting the proper PE system for a given application and how to perform PE in mammalian cells.
This protocol enables single-cell multi-omic analysis of the mouse brain immune compartment to explore immune cell heterogeneity and activation in the healthy and diseased brain, using a workflow based on HD flow cytometry, scRNA-seq and CITE-seq.
High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. This protocol describes pressure cycling technology (PCT)-assisted sample preparation of biopsy tissues.
A protocol is described for predicting the structures and functions of multi-domain proteins using the freely available deep-learning-based web platform I-TASSER-MTD.
Bacteria spheroid coculture allows long-term growth of bacteria in the hypoxic, necrotic core of tumor spheroids. This enables the study of bacteria–tumor interactions and rapid development of engineered microbial therapies.