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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.
Structural and functional analysis of human proteins requires their isolation in high yields and purity. Here, protease-cleavable, high-affinity, tag-specific nanobodies are used for the isolation of soluble and membrane proteins from lentiviral-transduced human cell suspensions.
This protocol enables genetic manipulation of nuclear and cytoplasmic giant viruses and their host, Acanthomoeba castellanii, by using either CRISPR–Cas9 or homologous recombination.
An X-ray microscopy approach for 2D or 3D label-free visualization of the intracellular distribution of nanomedicines and the morphology of organelles in primary blood cells, macrophages, dendritic cells, monocytes and cancer cells.
This protocol describes an assay to control mechanical forces during the natural flexion-extension cycle of the femorotibial joint of adult living fruit flies and to monitor fluorescent mechanosensitive reporters expressed in the neurons responsible for mechanosensation
This protocol provides guidelines for performing single-cell combinatorial indexing cleavage under targets and tagmentation. This method builds on the existing cleavage under targets and tagmentation method and uses a combinatorial indexing step to allow single-cell profiling of chromatin modifications.
This protocol describes the use of noninvasively triggered light in deep tissue via focused ultrasound-activated and systemically injected mechanoluminescent nanotransducers to achieve localized emissions with submillimeter resolution and millisecond response times.
A protocol detailing the assembly of an adaptive optics two-photon microscope setup and the guidestar-assisted shaping of the wavefront for imaging throughout the mouse neocortex at synaptic resolution.