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Split-GFP-based contact site sensors (SPLICS) are capable of reconstituting fluorescence when two opposing membranes come into close proximity. SPLICS can be used to quantify membrane contact sites between organelles in both fixed and living cells.
This protocol provides a step-by-step workflow for ATAC-Me, an integrated method for simultaneously probing DNA methylation and chromatin accessibility from a single DNA fragment library.
The polarity of gastrointestinal organoids is reversed to study epithelial biology and host–microbe interactions. Access to the apical surface of the epithelium is increased while preserving epithelial integrity and secretory and absorptive functions.
This protocol describes a scalable approach for joint profiling of chromatin accessibility and gene expression in single cells or nuclei that relies on multiple rounds of combinatorial indexing and can identify cell-specific regulatory elements.
This protocol explains how to use and apply COMETS (computation of microbial ecosystems in time and space), which extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments.
The authors present a protocol for expressing and biophysically characterizing rationally engineered SARS-CoV-2 spike proteins in Freestyle 293 and ExpiCHO cell lines.
This protocol describes a procedure for stabilizing and characterizing a transient high-energy RNA structure called the excited state, using relaxation dispersion NMR spectroscopy.
Structure-based docking screens of compound libraries are common in early drug and probe discovery. This protocol outlines best practices and control calculations to evaluate docking parameters prior to undertaking a large-scale prospective screen.
Quantitative MRI data acquired from patients with locally advanced breast cancer are used to calibrate a biophysical, reaction–diffusion mathematical model to predict response to neoadjuvant therapy on an individual patient basis.
Dysregulated growth and proliferation of tumors is related to metabolic changes. This protocol assesses metabolism in intact tumors using stable isotope-labeled nutrients delivered via bolus injection and continuous infusion in mice and humans.
This protocol describes a proteomic approach for efficient affinity capture, identification and quantification of endogenous phosphoprotein phosphatases and associated proteins from cells and tissues.
This protocol describes the use of Orthrus, an R package for processing, scoring and analyzing combinatorial CRISPR screening data, including data produced by the CHyMErA experimental system.
In this protocol, the authors describe CHyMErA (Cas hybrid for multiplexed editing and screening applications), a combinatorial genome-editing platform based on the co-expression of Cas9 and Cas12a nucleases in conjunction with a hybrid guide RNA.
This protocol describes how to load inorganic metal nanoparticles, drugs or radioisotopes into hollow nanocages composed of heavy-chain ferritin. The resulting formulations have intrinsic tumor-targeting capability and lack immunogenicity in vivo.
This multiplexed mass cytometry protocol uses thiol-reactive organoid barcoding in situ and a cytometry by time of flight signaling analysis pipeline (CyGNAL) to enable 126-plex single-cell analysis of cell type, cell state and post-translational modification signaling networks in organoids.
This protocol describes an LC-MS/MS assay and complementary web tool for analysis and prediction of intracellular accumulation of small molecules in E. coli based on their physiochemical properties, which could aid in future antibiotic discovery.
This protocol uses vascular corrosion casting, hierarchical synchrotron radiation microcomputed tomography imaging and computational image analysis to assess the 3D vascular network architecture in the entire postnatal and adult mouse brain.
The authors provide an optimized step-by-step protocol that uses mass cytometry to characterize well-known and emerging human dendritic cell populations in human blood and tissues. The protocol may also be applicable to other rare cell populations.
Bulk tumor preservation and dissociation enable multiple analyses of the brain tumor immune microenvironment via immunofluorescent staining and cell sorting followed by transcriptomics, genomics or in vitro culture of specific cell populations.
A protocol for quantitative MRI of the spinal cord using 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. The authors offer guidance for assessing macrostructural and microstructural integrity using various imaging approaches.