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Precise knowledge of the structure of metals supported and stabilized by zeolite frameworks informs improved design and synthesis of the catalysts. This tutorial describes scanning transmission electron microscopy approaches for their structural analysis.
The authors describe a platform to screen arrays of designer epigenome modifiers (DEMs) targeting up to three genes of interest using a multicolor reporter cell line to determine combinations producing the most efficient epigenome editing.
This protocol provides a detailed guide to metaproteomics data analysis and visualization. The modular and customizable workflow is based on two open-source tools (MetaProteomeAnalyzer and Prophane) and is illustrated with example datasets.
Mesoporous metal films are used in many electrochemical applications. This protocol describes how to make mesoporous Au, Pt and Pd films using micelle templates and provides examples of how to use them (glucose detection and catalysis for alcohol oxidation).
This protocol describes how to engraft human cancer cells in immunocompromised adult zebrafish. The fish are first adapted to 37 °C, followed by intraperitoneal or periocular muscle transplantation of xenograft cells and fluorescence imaging.
Here the authors describe a GUI-based protocol called FMAP for using funnel metadynamics to calculate the absolute binding free energy of a ligand to its molecular target and predict the ligand binding mode and mechanism.
This protocol describes how to engineer DNA nanostructures with different sizes, shapes and mechanical properties; load them with a siRNA cargo; and evaluate their ability to silence genes in mature tobacco plants.
This protocol describes the design and synthesis of CRISPR-responsive smart hydrogels and their actuation for both the controlled release of cargos (small molecules, enzymes, nanoparticles and living cells) and diagnostic applications.
This protocol describes a procedure for live-cell imaging of endocytic events in cultured cells using a pH-sensitive fluorophore and fast extracellular pH changes. A MATLAB-based analysis pipeline is provided to facilitate automated data processing.
The authors describe detailed procedures for an epigenomic profiling method suitable for low-input samples that is based on in situ labeling with an oligonucleotide-conjugated antibody.
GOTI (genome-wide off-target analysis by two-cell embryo injection) detects off-target mutations of CRISPR–Cas9-based genome editing and base editing. One blastomere of a two-cell mouse embryo is edited so that edited and unedited cells from the same genetic background can be compared.
This protocol describes a microfluidic platform for dynamic high-throughput analysis of the phenotypes of single cells. Cell-surface markers and secreted proteins are quantified and characterized by fluorescence detection using tailored immunoassays.
This protocol describes the MAC-tag approach, which combines affinity purification and biotinylation identification proximity labeling in a single tag. Binding proteins are identified by liquid chromatography–mass spectrometry, followed by visualization of protein localization using an online platform.
Embryonic stem cells undergo CRISPR–Cas9-mediated editing and are then used to reconstitute forebrain regions in mouse chimeras via neural blastocyst complementation.
Flow cytometry is used to track dynamics in microbial communities and link these changes with ecological parameters. This protocol describes how to prepare a fixed microbial cytometric mock community to standardize results over large-scale studies.
NAD+ is one of the noncanonical nucleotides recently found to cap the 5′ end of RNAs. This Protocol Extension describes procedures for genome-wide analysis of NAD+-capped RNAs by direct RNA sequencing on an Oxford Nanopore platform.
Formalin fixation and paraffin embedding (FFPE) of human tissue is a central strategy for preserving pathological specimens. This protocol describes how to process these specimens for spatially resolved LC-MS by laser-capture microdissection.
This protocol provides standardized laboratory manufacturing practices to select, cultivate and purify bacteriophages for human clinical applications. The procedure covers all stages from phage isolation and characterization to quality control.
Proteomic cysteines can undergo redox reactions and electrophile-derived modifications. In QTRP, a thiol-reactive probe is used to covalently label, enrich and quantify the reactive cysteinome in cultured cells and tissue samples.