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Peak table processing is essential for metabolomics, but finding the best workflow is challenging. This protocol describes NOREVA, an out-of-the-box software tool that can process and evaluate thousands of workflows in a single experiment.
This protocol describes a method for blood–brain barrier opening (BBBO) under the guidance of interventional MRI in mice. The method, which considerably reduces BBBO variability, can be used to improve delivery of therapeutics to the brain.
Many biological complexes are flexible or heterogeneous. Integrative modeling using Assembline enables structure determination of these macromolecular complexes by combining data from multiple experimental sources, including electron microscopy maps.
GUIDE-seq (genome-wide unbiased identification of double-stranded breaks enabled by sequencing) is a sensitive, unbiased, genome-wide method for defining the specificity of genome-editing nucleases in living cells.
This protocol describes experimental and computational procedures for genome-wide mapping of transcription factor binding at single-molecule resolution using methyl-transferase footprinting.
The trRosetta server, a web-based platform for fast and accurate protein structure prediction, is powered by deep learning and Rosetta. This protocol includes procedures for using the web-based server as well as the standalone package.
MALDI-TOF mass spectrometry (MS) can detect multiple compounds simultaneously. This protocol describes how to develop and optimize high-throughput, cell-based assays that use MALDI-TOF MS to detect drug uptake or biochemical markers of drug activity.
Human pluripotent stem cell aggregates are formed, embedded in Matrigel and directed to differentiate to heart-forming organoids by the chemical WNT pathway modulators CHIR99021 and IWP2.
Gouverneur et al. present a protocol for multigram synthesis of two chiral urea-based hydrogen-bonding phase-transfer catalysts for asymmetric nucleophilic fluorinations of target compounds, including detailed synthesis and purification procedures.
This two-phase task assesses the extent to which animals can discriminate and remember object locations. Unlike in similar tasks, the load on pattern separation during memory encoding—when pattern separation is thought to occur—varies.
Raman spectroscopy is increasingly being used in biological assays and studies. This protocol provides guidance for performing chemometric analysis to detect and extract information relating to the chemical differences between biological samples.
Yang and colleagues describe a rolling circle amplification-based approach for synthesizing multifunctional physically and dynamically cross-linked DNA hydrogels for efficient cell isolation and delivery.
Park and colleagues describe the synthesis of methacrylated photocurable silk fibroin bioink for digital light processing 3D bioprinting as well as fabrication of biocompatible organ-mimicking hydrogel structures for trachea tissue engineering.
Biological systems can now be studied at the single-cell level using mass spectrometry. In Single Cell ProtEomics (SCoPE2), a carrier sample is used to enhance peptide sequence identification with multiplexed analysis using isobaric mass tags.
The solution behavior of drugs is determined by NMR, enabling the presence of fast-tumbling lone drug molecules, small drug aggregates and slow-tumbling colloids to be determined.
Protein lipidation is challenging to analyze on the proteome level. This protocol describes metabolic incorporation of lipid probes and their capture via click chemistry, allowing in-gel fluorescence visualization or mass spectrometry analysis.
The authors present a magnetic purification protocol that separates scarce macropinosomes from other endocytic vesicles at a high purity and in an unbiased manner for label-free quantitative mass spectrometry.
The newly transcribed RNA-bound proteome (or RNA interactome) is captured using this protocol by time-dependent incorporation of 5-ethynyluridine into newly transcribed RNAs followed by UV-mediated RNA-protein cross-linking, click-chemistry-aided biotinylation and affinity isolation of RNA–protein complexes.