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Light-activated, 2,3-diaminopropionic acid-containing hydrolases trap substrate fragments, facilitating the discovery of new substrates and activities of enzymes in complex mixtures and live cells by mass spectrometry.
This protocol describes a CRISPR prime editing-based method for the sequential and unidirectional tracing of insertional events in mammalian cells, generating a dynamic recording of such information within living cells.
Scanorama is an effective tool for combining multiple single-cell RNA sequencing datasets, addressing technical variation introduced by differences in sample preparation, sequencing depth and experimental batches that can confound the analysis of diverse datasets.
Voltage-Seq is a method for all-optical voltage imaging-guided postsynaptic single-cell transcriptomics. It combines the use of the Voltron voltage indicator with the analysis tool VoltView to select specific neuronal somas to collect for single-cell RNA sequencing.
Conjugation of self-labeling enzymatic tags to axonal membrane proteins enables studying the dynamics of their trafficking, cellular localization and fate.
This protocol integrates genome-wide CRISPR knockout screening of toxins with in silico drug profiling for a new approach to targeted antidote development.
The morphological and molecular preservation of fresh-frozen tissues is difficult. Embedding with an hydroxypropyl methylcellulose/polyvinylpyrrolidone-rich hydrogel results in a material compatible with spatial biochemical analysis (e.g., mass spectrometry imaging), enabling multimodal data integration.
Untargeted mass spectrometry (MS) produces complex, multidimensional data. The MZmine open-source project enables processing of spectral data from various MS platforms, e.g., liquid chromatography–MS, gas chromatography–MS, MS–imaging and ion mobility spectrometry–MS, and is specialized for metabolomics.
This protocol presents ProBac sequencing, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets.
MSstats is used for the statistical analysis of proteomics data from DIA mass spectrometry experiments. This protocol describes workflows using (i) the MSstatsShiny graphical user interface and (ii) the R packages MSstats or MSstatsBig (for larger datasets).
Community-generated online templates for harmonized data reporting ensure that data and metadata associated with experiments are findable, accessible, interoperable, reusable and compiled for consistency in experimental design and test performance.
This protocol is for using xMarkerFinder, a four-stage computational framework, to enable the identification and validation of reproducible microbial biomarkers from cross-cohort studies, and establish potential microbiome-induced mechanisms.
This protocol presents a metabolomics method tailored for detecting and measuring gut-microbe-derived metabolites using a broad reference library of metabolite standards.
This protocol describes toxin activation–inhibition conjugation (TAC–TIC), a reverse genetics screening approach that can be used to identify triggers or blockers of bacterial toxin–antitoxin or phage immunity systems.
The buildup and operation of a custom single-molecule localization microscope with state-of-the-art performance and advanced features bridges the gap between entry-level open-source projects and costly commercial systems.
This protocol details the generation of cortical organoids with complex neural oscillations through a ‘semi-guided’ protocol, and their functional characterization using microelectrode array measurements, calcium imaging and adeno-associated virus transduction.
Ancient proteins carry genetic information from fossils that are too old or degraded for ancient DNA recovery. This protocol describes the extraction and tandem mass spectrometry sequencing of million-year-old dental enamel proteins for phylogenetic inference.
This protocol details methods for using methanol in methylation reactions, including the synthesis of suitable transition metal-containing catalysts, and in the synthesis of heterocycles. The methods described produce only H2 and H2O as by-products.
Isotope ratio mass spectrometry as described in this protocol can be used to determine natural variation in the abundance of stable isotopes in individual compounds to provide information relevant to metabolism, ecology or climate change.
Surface photovoltage microscopy as described in this protocol allows high spatial and energy resolution mapping of surface-charge distributions on photocatalyst particles, enabling rational design of improved materials.