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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.
The authors describe an easy-to-follow bioinformatic pipeline, called EpiTyping, for the identification of abnormal biallelic expression of imprinted genes and the analysis of the X-chromosome inactivation state from RNA sequencing data obtained from human pluripotent stem cells.
This Perspective covers recent advances in mass spectrometry and explains how these approaches may be used to study the structure and function of protein condensates undergoing liquid–liquid phase separation.
The procedure details the preparation of mixed bone marrow radiation chimeras for the labeling of osteoclasts and osteomorphs, and the imaging of the mouse tibia for the longitudinal study of endosteal and bone marrow niches.
The assembly and organization of functional cargo using synthetic DNA scaffolds on biomaterials enable precise presentation of modulatory signals to immune cells.
18F-labeled cysteine residues, synthesized via metal-free radiodeoxyfluorination, and 18F-labeled ruthenium-containing peptide sequences, via ruthenium-assisted radiodeoxyfluorination, can be used as tracers for positron emission tomography imaging.
Structure-based virtual screening via docking can find molecules strongly binding to a target. This protocol describes how to use machine learning to improve this by building a target-specific scoring function and evaluating it on that target.