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This protocol describes nanoflow liquid chromatography–mass spectrometry (nanoLC-MS) analysis of the N-glycans and O-glycans of glycoproteins and glycolipids, as well as site-specific glycosylation of membrane proteins.
In this protocol, the authors describe the design, fabrication, purification, characterization and potential biomedical applications of a self-assembling TDN-based multifunctional delivery system.
This protocol describes procedures for isolating the protein-bound transcriptome and RNA-binding proteome via UV crosslinking and organic/aqueous phase separation.
This protocol offers a CRISPR-based toolkit, including several variants of ‘classic’ CRISPR–Cas9, along with CRISPRi and CRISPR-base editing systems (CRISPR-BEST) for genome editing in streptomycetes.
This protocol describes a lentivirus-based massively parallel reporter assay (lentiMPRA) for quantitative assessment of the activity of gene regulatory elements and an accompanying Nextflow-based computational pipeline for analysis.
Pupil diameter is measured in rodents using low-cost cameras and a Raspberry Pi computer to obtain a rapid, noninvasive real-time readout of locus coeruleus activity.
This protocol describes how to perform geometric morphometrics on microscopic animals, as exemplified by analysis of nematode mouth morphology. The procedure provides guidance for microscopy data acquisition, data analysis and validation.
This protocol describes an approach for quantitative analysis of membrane deformations by purified proteins at a single-molecule level. Changes in luminal conductance of ultra-short (80- to 400-nm) lipid nanotubes are used as real-time reporters.
This protocol describes a ChIP-seq procedure optimized for profiling H3K27 acetylation in archived formalin-fixed, paraffin-embedded (FFPE) tissues sampled through whole or macrodissected sectioning or from punched cores.
In pseudotargeted metabolomics, transitions used for multiple-reaction monitoring are chosen from mass spectrometry data obtained using mixtures of real samples. Semiquantitative information is obtained without knowing the identity of the compounds.
An aptamer-trigger-clamped hybridization chain reaction (atcHCR) captures tumor cells in a protective, porous, 3D DNA hydrogel. Subsequent addition of ATP facilitates release of the tumor cells for use in downstream assays.
This protocol describes an in vitro assay for studying how phagocytosis is affected by specific changes to the target surface. The targets are made by coating glass beads with supported lipid bilayers followed by coupling proteins and other ligands of interest.
SCENIC is a computational pipeline to predict cell-type-specific transcription factors through network inference and motif enrichment. Here the authors describe a detailed protocol for pySCENIC: a faster, container-based implementation in Python.
Optimizing the synthesis of chiral compounds involves determining the enantiomerical excess (e.e.) of the products. This protocol describes a high-throughput fluorescence-based assay to determine the e.e. of diols, amino alcohols, and amines.
fMRIPrep is an open-source software tool to ready fMRI datasets for statistical analysis and modeling that is robust to a diversity of inputs and produces standardized outputs, facilitating aggregation of data across studies.
This protocol describes how to characterize the 3D topology of long noncoding RNAs. The authors provide detailed step-by-step procedures for the complete workflow from lncRNA isolation to AFM imaging and SAXS analysis.
Ice formation has hindered organ preservation below 0 °C. In this protocol, human livers are preconditioned with cryoprotective agents during machine perfusion and then supercooled to avoid ice formation.
This protocol details the assembly and use of the wide field-of-view nematode tracking platform (WF-NTP), which enables the simultaneous analysis of thousands of worms with respect to multiple behavioral parameters.
This protocol describes how to construct and use an open-source robot for automatically performing cranial microsurgeries such as skull thinning and various-sized craniotomies in mice.
High-resolution structural analysis of macromolecular complexes by cryo-ET requires extremely thin samples. This protocol describes how to prepare thin specimens using FIB milling from frozen cells on grids, which enables direct structural analysis of biomolecules in their native environments, i.e., cells.