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Branched fatty acid esters of hydroxy fatty acids (FAHFAs) are a recently discovered class of biological lipids. This protocol describes their extraction from serum and tissue samples, followed by enrichment and analysis by LC-MS.
Upconversion nanoparticles (UCNs) have the extraordinary ability to emit light with UV-visible wavelengths on illumination in the near IR region. This protocol describes the preparation of UCNs with potential therapeutic applications.
Raman microspectroscopy is useful for the analysis of biological samples, because chemical and structural information can be obtained without using labels. This protocol brings together practical guidelines from expert research groups.
This protocol from Hassan et al. describes a microfluidic chip that uses an immunocapture chamber to count CD4 and CD8 cells in whole blood for HIV/AIDS diagnostics. The chip can be adapted for different cell types and research applications.
Interferometric scattering microscopy (iSCAT) enables ultrasensitive label-free imaging and high-speed single-particle tracking. This protocol describes how to construct an iSCAT microscope with single-molecule TIRF capabilities.
Annexin A5 and TO-PRO-3 (a nucleic acid–binding dye that stains early apoptotic and necrotic cells differentially) are used to distinguish six types of particles in a sample, including apoptotic bodies and cells at various stages of cell death.
This protocol describes how to set up and use the autopatcher, a robot that automatically obtains intracellular neural recordings from intact mammalian mouse brains.
Transcription factories contain all three mammalian RNA polymerases, each actively transcribing a different subset of genes. This protocol describes how to isolate large factory fragments for the analysis of associated protein and RNA content.
This protocol describes how to use miniature, integrated microscopes in conjunction with an implantable microendoscopic lens to guide light into and out of the brain, thereby enabling optical access to the brain.
Genome editing using designer nucleases such as TALENs or the CRISPR-Cas9 system is hampered by a lack of methods to detect and quantify the products. Here the authors present GEF-dPCR, a droplet-based digital PCR method for assessing gene-editing frequencies.
Venous access catheters used in clinics are prone to biofilm contamination, contributing to chronic infections. Here the authors provide a protocol to allow the in vivo study of catheter-associated biofilm infections in a TIVAP rat model.
This protocol describes how to sequence the transcriptome from a single nucleus. It is particularly suited to cell types that are difficult to isolate as intact whole cells, such as neurons.
This protocol describes how to reconstruct and culture the freshwater rainbow trout gill epithelium. This model can be used to study gill physiology and has applications in toxicity testing, bioaccumulation studies and water quality monitoring.
In this protocol, Hung et al. describe a method for performing cell compartment–specific proteomics for regions of interest using the engineered ascorbate peroxidase APEX2.
Canfarotta et al. describe an elegant molecular imprinting method in which the target is immobilized on glass beads. These are then used to produce nanoparticles, with binding properties analogous to those of antibodies.
Here the authors describe cP-RNA-seq to selectively amplify and sequence cyclic phosphate (cP)-containing RNAs. This method extends the utility of standard RNA-seq to the assessment of cP-containing RNA repertoires in various transcriptomes.
mNET-seq generates genome-wide, single-nucleotide–resolution data on Pol II occupancy and co-transcriptional RNA processing, with the unique ability to link these processes to Pol II C-terminal domain phosphorylation states.
This protocol uses a microfluidic flow-focusing device to encapsulate single cells, enabling high-throughput sequencing of the paired immune receptor repertoire from millions of lymphocytes at the single-cell level.
5PSeq is a method for studying ribosome dynamics based on co-translational mRNA decay. Genome-wide sequencing and quantification of 5′ phosphorylated mRNA degradation products allows the positions of the last translating ribosomes to be determined.