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Feature-based molecular networking is used to analyze non-targeted liquid chromatography–tandem mass spectrometry metabolomics data. This protocol includes instructions, ready-made code and a web app (https://fbmn-statsguide.gnps2.org/) for statistical analysis of feature-based molecular networking results.
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.
We present a practical workflow for end-to-end weakly supervised deep learning to predict biomarkers directly from whole-slide images, enabling clinical researchers to work with engineers to set up a complete computational pathology project.
CellChat enables systematic inference, quantitative analysis and intuitive visualization of cell–cell communication from single-cell transcriptomic data, as well as comparative analysis of intercellular communication across biological conditions.
A cost-effective, facile, versatile and ultrafast methodology to fabricate perfusable microchannels of complex shapes in photopolymerizable hydrogels without the need for specialized equipment or sophisticated protocols.
Protocol for the generation of a stem cell-derived human postimplantation embryo model by the combination of embryonic and transgene-induced extraembryonic-like cells.
This protocol covers the production and construction of new-generation transmorphic phage/adeno-associated virus vectors for the systemic delivery of nucleic acid payloads. In vitro and in vivo applications of transmorphic phage/adeno-associated virus particles are also discussed.
This protocol for the precise tracking of nanoparticles in plant roots uses CLSM for macroscopic tissue examination and TEM for cellular-level analysis and provides methodologies for preparing plant materials before imaging.
DiMeLo-seq uses long-read, single-molecule sequencing to map protein–DNA interactions genome wide. This allows mapping of multiple interaction sites on single DNA molecules and profiling protein binding in the context of endogenous DNA methylation.
The three methods present visualize epigenetic modifications and their spatial proximities in single cells; base-encoded amplifying FISH, pairwise proximity-differentiated amplifying FISH and cellular macromolecules-tethered DNA walking indexing.
High-resolution diffusion uses a dense optical flow algorithm to quantify and classify the motion of nuclear macromolecules, assigning biophysical parameters such as the diffusion constant, the anomalous exponent and the drift velocity.
STRAIGHT-IN is a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines through targeted integration of a DNA payload into a landing pad, which is achieved with minimal scarring.
Nitrogen heterocycles are a large class of chemically and biologically relevant compounds. This protocol describes their synthesis from alcohols using homogeneous iridium/ruthenium catalysts and heterogeneous cobalt/copper catalysts.
This protocol describes the generation of cyborg bacterial cells by using intracellular hydrogelation. These nondividing, stressor-resistant engineered bacteria chassis can find application as living environmental biosensors and in disease treatment.
Proximity sequencing uses a panel of antibodies to probe single cells for up to hundreds of targets simultaneously. The approach is capable of detecting targets that are located within 50–70 nm of each other and thus likely to form complexes.
nPOP is a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides by using the CellenONE instrument. This protocol describes the liquid handling for multiplexed mass spectrometry proteomics.
This protocol describes a flux synthesis approach for two-dimensional covalent organic frameworks. Compared with other approaches, this method does not use solvents, making it environmentally friendly, and is scalable up to the kilogram scale.
BANC-seq enables quantification of genome-wide transcription factor binding affinities in the native chromatin context. This protocol describes implementations based on chromatin immunoprecipitation or cleavage under target and release using nuclease, followed by library preparation, sequencing and data analysis.
The transplantation of human cortical organoids in rats enables maturation and integration of human neural cells that can engage with the host circuitry, providing a framework to study alterations in morphology and physiology of patient-derived tissue.
This protocol describes the use of iPhone LiDAR to generate high-resolution 3D models for topographic surveying and to measure their changes over time. The protocol simplifies the use of the iPhone LiDAR sensor, making it accessible to non-experts.