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This protocol describes procedures for high-throughput analysis of trigenic interactions in yeast. Triple-mutant strains generated in a series of automated replica-pinning steps are grown on agar plates as individual colonies, and interactions are quantified with the trigenic synthetic genetic array scoring method.
This protocol describes how to perform near-infrared spectroscopy and imaging of connective tissues. Detailed guidelines are provided for sample preparation, spectral acquisition and data pre-processing and analysis, with example applications.
The authors describe a modular pipeline to detect aberrant gene expression events (expression level, splicing and mono-allelic expression) from patient RNA sequencing data, which can complement DNA-based diagnosis by enhancing the functional interpretation of variants.
This protocol for base editing in cultured mammalian cells provides guidelines for choosing target sites, appropriate base editor variants and delivery strategies, as well as detailing the computational analysis of base-editing outcomes using CRISPResso2.
This protocol describes how to perform combined protein isoform detection with nucleic acid analysis from the same individual mouse embryo or blastomere using fractionation polyacrylamide gel electrophoresis (fPAGE).
A protocol for implementing Brillouin microscopy to study biological materials. The procedure contains instructions for integrating an add-on Brillouin module with an existing confocal microscope as well as for its calibration and use in data collection and processing.
Reversible protection of the primary face of cyclodextrins by silylation is a very popular strategy for modification of the secondary rim. This protocol describes how to prepare these important intermediates in high yield and purity.
This Protocol Extension presents recombinant extracellular vesicles as reference materials for method development and standardization. It details their characterization and detection in spiked samples by fluorescence, nucleic acid and protein measurements.
Cultivating native bacteria from fresh plant roots is essential for understanding their interaction with the host plant. This protocol describes their isolation and accurate taxonomical identification using two-sided barcode polymerase chain reaction and Illumina sequencing.
The authors describe hardware setup and experimental workflows for collecting and analyzing the biotic and abiotic environmental exposome at the individual level.
This protocol describes an approach to quantifying DNA replication dynamics (initiation and termination frequencies and origin firing efficiencies) at defined genomic loci in asynchronously growing cells.
A new protocol for solid-state NMR of soluble and membrane proteins in E. coli, in both whole cells and isolated membrane fractions. The procedure describes conventional 13C/15N ssNMR as well as sensitivity-enhanced DNP-ssNMR and 1H-detected ssNMR.
This protocol describes VAMPIRE, an unsupervised machine-learning approach that can be used to quantify and categorize cellular morphology from fluorescence or bright-field images of cells grown in 2D, 3D and tissue slices.
Mancuso and De Strooper and colleagues describe MIGRATE (microglia in vitro generation refined for advanced transplantation experiments, a combined in vitro differentiation and in vivo xenotransplantation protocol for studying human microglia transplanted into mouse brain.
Optimization of chemical reactions can be facilitated by techniques that enable experiments to be set up in parallel. In this work, 96 Pd–catalyzed cross-coupling experiments are performed and analyzed in parallel with commonly available equipment.
The authors discuss experimental design considerations and describe a computational pipeline to reveal the synergistic and additive effects of combinatorial perturbations on gene expression measured by RNA sequencing.
Takebe et al. describe a protocol for the continuous patterning of hepatic, biliary and pancreatic structures from a 3D culture of human pluripotent stem cells.