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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.
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.
This protocol describes the generation of single-clone viral stocks from patients with severe acute respiratory syndrome coronavirus 2, from the isolation of samples from patient swabs to the purification of specific clones, quality control and the generation of working stocks.
Combinatorial fluorescent labeling of anaerobic (and aerobic) bacterial strains using azide-modified sugars for macromolecular synthesis and a biorthogonal reaction for the cycloaddition of multiple fluorophores, suitable for use in anaerobic conditions.
There is increasing concern about the harmful effects of micro- and nanoplastics (MNPs). This protocol describes how to generate MNP samples and perform ecotoxicity experiments by taking into account their physicochemical properties and behavior.
An integrated workflow for multiplexed tissue image processing and analysis, including interactive inspection of raw data, cell segmentation, feature extraction, single-cell analysis and spatial analysis.