Protocol Extension

A protocol extension describing the purification of prenatal human brain endothelial and mural cells with FACS and their utilization in downstream applications, including cell culture, organoid transplantation and single-cell transcriptomics.

This protocol presents a workflow for the enrichment of plant nuclei from cells targeted by pathogenic bacterial effectors during bacterial infection.

This Protocol Extension combines optogenetics with juxtacellular recordings and describes procedures for targeting, recording and labeling individual genetically defined neurons in freely moving mice.

This Protocol Extension describes Zebrafish targeting of Reactive Electrophiles and oXidants (Z-REX), an extension of a Protocol on the targetable reactive electrophiles and oxidants, adapted for on-demand redox targeting in live zebrafish embryos. The protocol details how to generate transgenic fish and run Z-REX, as well as its downstream validation.

This Protocol Extension describes an operant model in which mice lever press to obtain rewarding social interaction with a peer. The model can be used to study the role of operant social reward and other neuropsychiatric disorders with a component of social dysfunction.

This Protocol Extension presents an updated tetrahedral DNA nanostructure for the delivery of various bioactive molecules that enables an active targeting strategy to be used for stimuli-sensitive conformation changes and on-site cargo release.

This Protocol Extension describes the fabrication and implantation of 3D-printed neural probes for tethered or wireless optogenetics in freely moving rodents.

This extension of the TCP-seq protocol describes procedures for selective profiling of 40S and 80S ribosome subpopulations bound by a factor of interest, permitting detailed studies of the different stages of translation in mammalian and yeast cells.

This protocol describes how to use the free, vendor-neutral software Skyline to process and annotate multidimensional lipidomic data by using expanded features such as predicted retention times, spectral libraries and ion mobility filtering.

LC–HRMS is used for metabolomics studies in the biomedical and environmental sciences. MetaboAnalyst (metaboanalyst.ca) can be used to address challenges in data processing, statistical analysis, functional interpretation and multi-omics integration.

This Protocol Extension (to an existing SELEX Nature Protocol) introduces RNA G-quadruplex (rG4)-SELEX, a method that generates novel l-RNA aptamers to target rG4 structures that can be applied to inhibit G-quadruplex-mediated interactions.

This protocol extension describes the GFP thermal shift assay for monitoring ligand interactions of solute carrier transporters using either crude detergent-solubilized membranes or purified samples.

This Protocol Extension discusses several approaches to analyzing clonogenic growth of mammalian cells in vitro, using a modular framework to facilitate the use of various formats to fully optimize clonogenic growth.

The authors present a protocol for testing physiologically relevant infection conditions (e.g., lung and wound exudate or blood) in minimal inhibitory concentration (MIC) assays.

This extension of a previous in vitro digestion protocol provides a subsequent in vitro batch fermentation stage that is carried out afterward to enable investigation of the effect of food on the gut microbiome.

Here, we present a protocol for high-throughput screening of SPOT-peptide arrays to assess the antibiofilm, antimicrobial and immunomodulatory activities of synthetic peptides.

This Protocol Extension details the use of zebrafish larvae as a simple and robust in vivo system for studying human norovirus infection, enabling evaluation of the antiviral effects and toxicities of small molecules.

This protocol describes how to direct differentiation of human pluripotent stem cells in a 3D matrix of collagen I to cultures containing mature alveolar type II and I cells plus airway basal, ciliated, club and neuroendocrine cells.

In this extension to their NET-seq protocol, the authors combine isolation of 4sU-labeled chromatin-associated nascent RNA with long-read direct RNA sequencing on nanopores to profile the kinetics and patterns of co-transcriptional RNA processing.

This Protocol Extension presents recombinant extracellular vesicles as reference materials for method development and standardization. It details their characterization and detection in spiked samples by fluorescence, nucleic acid and protein measurements.