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This protocol presents a comprehensive workflow for the implementation of whole-genome sequencing in routine tumor diagnostics, exemplified by the pipeline used in the Netherlands Cancer Institute.
The recently available 28.2 Tesla nuclear magnetic resonance spectrometers (1.2 GHz 1H frequency) can be used to characterize highly flexible proteins and protein regions. This protocol explains how to setup 13C nuclear magnetic resonance experiments to achieve optimal results.
An automated workflow for culturing human induced pluripotent stem cells expressing fluorescently tagged proteins, and seeding them on 96-well optical-grade, glass-bottom plates for high-quality, live-cell three-dimensional microscopy on a large scale.
A protocol detailing the labeling and identification of cell- and subcompartment-specific proteins found within intact astrocytes and neurons in vivo using the proximity-dependent biotinylation system BioID2.
This article describes the main sources of bias in small RNA-sequencing and the importance of obtaining structure-level information for the correct interpretation of high-throughput sequencing results.
A protocol describing how to implant head-mounted jugular vein catheters in mice. This procedure facilitates systemic drug administration in a variety of experimental settings, including optical recording and manipulation of neuronal activities and behavioral tests.
Two-dimensional protein films, prepared via amyloid-like aggregation, can be made with nano- to meter-scale dimensions and features such as high interface adhesion, as well as tunable antibacterial, biomineralization and antifouling activity.
Tail-to-head terpene cyclization is an essential reaction for terpene synthesis, but it is difficult to achieve without an enzyme. This protocol describes the preparation and use of a hexameric resorcin[4]arene capsule as an artificial enzyme.
This protocol for the spatiotemporal control of RNA activity uses LicV, a synthetic, photoswitchable RNA-binding protein (RBP) that can bind to a specific RNA sequence in response to blue light irradiation, and provides an efficient and generalizable strategy for engineering photoswitchable RBPs.
This protocol describes a reproducible and reliable method for excisional skin wound healing assays in mice. The use of lineage-tracing assays to investigate the contribution of different cell populations to the repair process is also discussed.
CONIPHER is a computational framework for accurately inferring subclonal structure and the phylogenetic tree from multisample tumor sequencing, accounting for both copy number alterations and mutation errors.
This protocol describes barcoding bacteria for identification and quantification, a method for identifying and quantifying bacterial cells in microbiota samples based on the droplet-based barcoding and amplification of 16S rRNA genes from single bacterial cells.
Angstrom-scale two-dimensional channel devices can be assembled with precise control over their dimensions, as a single channel or hundreds of channels using layered crystals, and enable the measurement of angstrom-scale gas, ion and water fluidics.
Obtaining large, uniform crystals of polymer materials, including covalent organic frameworks, is challenging. This protocol describes a fast, effective approach to making crystalline two- and three-dimensional covalent organic frameworks using supercritical CO2 as the solvent.
This protocol presents a computational approach to scoring drug sensitivity that integrates multiple dose–response parameters into a single response metric and identifies differences in drug-response patterns between cancer cells and healthy control cells.
Single-cell multiple displacement amplification with the variant caller SCcaller ensures high-fidelity, quantitative analysis of single-nucleotide variations and small insertions and deletions.
This protocol describes procedures for learning cellular and molecular processes from single-cell RNA-sequencing data using the non-negative matrix factorization algorithm Coordinated Gene Activity across Pattern Subsets. Parallel analysis is demonstrated in Python, R and GenePattern Notebook.
Mitochondrial protein assemblies are vital for neuronal and brain function. This protocol describes a co-fractionation–mass spectrometry platform to study native motochondrial assemblies in brain and cultured nerve cells after chemical cross-linking.