Volume 18 Issue 12, December 2023

A protocol for assembling complete mouse embryo models from embryonic and induced stem cells to generate advanced embryonic and extraembryonic organs.

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.

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.

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.

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.

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.

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 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.

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.