Research articles

This protocol extension guides users in identifying candidate drug metabolites without prior knowledge by analyzing tandem mass spectrometry data in the web-based molecular networking tool GNPS2.

We present a protocol for the design, fabrication and use of a microfluidic probe for nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) that achieves a spatial resolution of 8–10 µm and 10-fold improvement in experimental throughput.

This protocol details the generation and characterization of vestibular inner ear organoids from human pluripotent stem cells. This is an extension of a previous protocol for skin organoid generation, with which it shares foundational methodology and reagents.

This protocol extension enables researchers to integrate optically based manipulation and measurement techniques into their touchscreen experimental systems, focusing on optogenetic manipulation, fiber photometry and microendoscopic imaging.

This is a Protocol extension describing the establishment of human expanded potential stem cell lines from preimplantation embryos or by reprogramming somatic cells and their validation and characterization.

In this Protocol Extension, the authors describe procedures for spatial barcoding in tissue sections using a microfluidic chip followed by sequencing-based joint genome-wide profiling of transcriptome and open chromatin or histone modifications.

Behavior-guided transcriptomics is an extension to the BEHAV3D protocol, for the integration of T cell live-imaging data with single-cell transcriptomics, enabling analysis of gene programs linked to dynamic T cell behaviors.

We present a protocol detailing the extraction and quantification of glycosaminoglycans extracted from biofluids by using ultra-high-performance liquid chromatography combined with triple-quadrupole mass spectrometry.

This protocol extension details two approaches to creating a bioswitchable delivery system for microRNA therapeutics, based on a tetrahedral DNA nanostructure with a ribonuclease H-sensitive sequence as a bioswitchable apparatus for the controlled release of cargo.

The authors present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissue and using them in a single-vesicle fusion assay to examine their association and fusion with plasma membrane mimic vesicles.

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.