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This protocol presents a method for single-cell RNA sequencing of tissue-resident murine eosinophils, with a complementary method for CRISPR screening of bone marrow-derived eosinophils.
BEHAV3D is a 3D live imaging platform for analyzing engineered T cell behavior and tumor response. This provides insights into the mode of action of cellular immunotherapy, capturing heterogeneity within and between tumors during treatment response.
MXenes are two-dimensional materials with diverse optoelectronic, biological, mechanical and chemical properties. This protocol describes how to prepare single-layer flakes of Ti3C2Tx, the most important and widely used MXene, from a Ti3AlC2 MAX phase precursor.
Synteny and colinearity are important parameters that delineate the evolution of genomes and gene families. This protocol describes MCScanX, a user-friendly toolkit that facilitates rapid evolutionary analysis of chromosomal structural changes.
Transkingdom Network Analysis (TkNA) is a unique analytical framework for inferring causal factors underlying host–microbiota and other multi-omic interactions, by integrating data from multiple cohorts and diverse omics types.
Ultra-stable magnetic tweezers allow measuring individual protein dynamics in equilibrium under physiologically relevant pulling forces and over timescales of days to weeks, enabling high-precision molecular studies in mechanobiology.
Atomic force microscopy can be used to determine the stiffness of materials. This protocol describes how to measure and quantify the Young’s modulus E of pulmonary mouse and human basement membranes with atomic force microscopy and the Center for Applied Tissue Engineering and Regenerative Medicine processing toolbox.
We provide a twisting fabrication process for fiber electrodes that can be assembled into electronic threads and then integrated in electronic textile-based wearables.
The authors describe how to prepare antimicrobial phage-based microgels, using polystyrene film templates, and detail their use to kill antibiotic-resistant bacteria in food contamination tests as an example application.
Optimization of chemical transformations involves screening numerous reaction parameters. This protocol outlines how screening experiments can be rapidly and economically analyzed by quantitative benchtop 19F NMR spectroscopy.
Phylogenetic trees from whole-genome sequencing datasets with the pipeline Sequoia are reconstructed to define the evolutionary history of clonally expanding cells and to clarify how somatic mutations shape normal cell behavior.
This protocol provides detailed guidelines for using rMATS-turbo—the latest implementation of the popular software for the discovery and quantification of alternative splicing events from RNA sequencing data—exemplified in two representative scenarios.
This protocol details a method for profiling the glycosylation status of antigen-specific antibodies. The protocol consists of an antibody-capture step using an immunosorbent assay similar to enzyme-linked immunosorbent assay, followed by the characterization of captured antibodies using liquid chromatography–mass spectrometry.
This multi-omics data integration protocol, which uses the web-based Analyst tool suite, covers knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction.
A protocol for Nano-DMS-MaP, a method for in situ isoform-specific RNA structure determination. The technique employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules, revealing previously hidden structural differences.
We provide a detailed roadmap for scientists interested in performing FDTD computational simulations to probe the interactions of electromagnetic waves (e.g., visible light or microwave radiation) with complex structures such as organs or biological cells.
The authors introduce MACHETE (molecular alteration of chromosomes with engineered tandem elements), a clustered regularly interspaced short palindromic repeats directed Cas9-based system for the efficient deletion of megabase-sized genomic regions.
The controlled positioning and stoichiometry of aptamers on tetrahedral DNA frameworks enables the synthesis of targeted probes for the capture of circulating tumor cells from blood samples.
FiLa biosensors allow real-time subcellular analysis of lactate metabolism. This protocol describes their preparation and characterization, and their use in in vitro and in vivo assays, under various nutritional and pharmacological conditions.