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RNA-binding proteins orchestrate many aspects of plant development and environmental responses. This protocol describes an optimized plant individual-nucleotide-resolution cross-linking and immunoprecipitation method for genome-wide identification of RNA-binding protein binding sites on their cognate RNAs at single-nucleotide resolution.
This protocol describes a method for sampling the microbiome of food-processing facilities and analyzing it by using whole-metagenome sequencing. The protocol includes sampling and DNA-extraction and DNA-purification steps optimized for low-biomass samples.
A detailed workflow covering 3D pathology, including tissue preparation, imaging with light-sheet fluorescence microscopy, tools for initial data processing in Python (e.g., stitching, intensity leveling and false coloring) and data quality control.
A web-based tool to guide the lead optimization process by improving calculation of substructure modifications of candidate compounds with improved absorption, distribution, metabolism, excretion, and toxicity profiles.
The formation and functional relevance of N6-methyladenosine sites are key unanswered questions in the field of RNA biology. The protocol describes an unbiased sequencing-based method for the characterization of the global distribution and stoichiometry of N6-methyladenosine sites.
Light-activated assembly of split-protein fragment pairs using the covalent SpyTag/SpyCatcher peptide–protein reaction can be used to modulate biological protein activity in solution, biomaterials and cells.
Antigen-specific B cells constitute a small proportion of the total B cell population, making identification for downstream analysis challenging. Here, this is achieved by pairing fluorescent antigen tetramer probes with a sensitive enrichment approach.
A customized hyperspectral confocal microscope enables the tracking of living cells and sensing of cellular processes by characterizing bio-integrated microlasers with high spectral resolution.
Genome-scale metabolic models enable mathematical exploration of metabolism under various defined conditions. This protocol describes GECKO, a method for enhancing a genome-scale metabolic model with enzymatic constraints using kinetic and omics data (e.g., proteomics).
This protocol provides extensive guidelines and detailed steps to generate novel bio-engineered bacterial strains using CRISPR-associated transposase (CAST) systems, with available plasmids and standard molecular biology techniques.
A light sheet fluorescence microscopy approach for the analysis of immune cell composition, vascularization, tissue perfusion and hypoxia enables spatial imaging of the tissue microenvironment in cancer and cardiovascular diseases.
The procedure guides inexperienced users interested in handling spatial omics data in a Python environment to streamline data analysis and to facilitate benchmarking analysis via the spatial omics database.
Mapping of chromatin states at single-cell resolution is still challenging. This protocol describes nano-CT, a novel method to simultaneously characterize up to three epigenetic modalities at single-cell resolution.
The detailed design and fabrication of small-scale magnetic soft-bodied robots with multimodal locomotion capability, including the processes required for locomotion control and optimization.
The authors describe a high-throughput screening strategy that can be carried out anaerobically for studying the effects of drugs in vitro on individual gut microbes or microbial communities created synthetically or obtained from stool samples.
This protocol presents a comprehensive workflow for the implementation of whole-genome sequencing in routine tumor diagnostics, exemplified by the pipeline used in the Netherlands Cancer Institute.
The recently available 28.2 Tesla nuclear magnetic resonance spectrometers (1.2 GHz 1H frequency) can be used to characterize highly flexible proteins and protein regions. This protocol explains how to setup 13C nuclear magnetic resonance experiments to achieve optimal results.
An automated workflow for culturing human induced pluripotent stem cells expressing fluorescently tagged proteins, and seeding them on 96-well optical-grade, glass-bottom plates for high-quality, live-cell three-dimensional microscopy on a large scale.
A protocol detailing the labeling and identification of cell- and subcompartment-specific proteins found within intact astrocytes and neurons in vivo using the proximity-dependent biotinylation system BioID2.
A protocol describing how to implant head-mounted jugular vein catheters in mice. This procedure facilitates systemic drug administration in a variety of experimental settings, including optical recording and manipulation of neuronal activities and behavioral tests.