Volume 16 Issue 10, October 2021

This protocol uses vascular corrosion casting, hierarchical synchrotron radiation microcomputed tomography imaging and computational image analysis to assess the 3D vascular network architecture in the entire postnatal and adult mouse brain.

A protocol for quantitative MRI of the spinal cord using 3T MRI systems from the three main manufacturers: GE, Philips and Siemens. The authors offer guidance for assessing macrostructural and microstructural integrity using various imaging approaches.

This protocol comprises various methods to coculture organoids (particularly human small intestinal and colon organoids) with microbes, including microinjection into the lumen and periphery of 3D organoids and exposure of organoids to microbes in a 2D layer.

This protocol describes how to undertake high spatial and temporal Ca²⁺ imaging of ex vivo multicellular myocardial strips that include the endocardial surface, allowing the study of the Ca²⁺ signaling that underpins cardiomyocyte contraction.

This protocol outlines the experimental and computational steps of MetaRibo-Seq, a modified ribosome profiling approach that allows direct interrogation of translation in uncultured bacterial communities.

Bulk tumor preservation and dissociation enable multiple analyses of the brain tumor immune microenvironment via immunofluorescent staining and cell sorting followed by transcriptomics, genomics or in vitro culture of specific cell populations.

In this protocol, the authors describe CHyMErA (Cas hybrid for multiplexed editing and screening applications), a combinatorial genome-editing platform based on the co-expression of Cas9 and Cas12a nucleases in conjunction with a hybrid guide RNA.

This protocol describes the use of Orthrus, an R package for processing, scoring and analyzing combinatorial CRISPR screening data, including data produced by the CHyMErA experimental system.

Structure-based docking screens of compound libraries are common in early drug and probe discovery. This protocol outlines best practices and control calculations to evaluate docking parameters prior to undertaking a large-scale prospective screen.

This protocol describes an LC-MS/MS assay and complementary web tool for analysis and prediction of intracellular accumulation of small molecules in E. coli based on their physiochemical properties, which could aid in future antibiotic discovery.

The authors provide an optimized step-by-step protocol that uses mass cytometry to characterize well-known and emerging human dendritic cell populations in human blood and tissues. The protocol may also be applicable to other rare cell populations.

This protocol describes how to load inorganic metal nanoparticles, drugs or radioisotopes into hollow nanocages composed of heavy-chain ferritin. The resulting formulations have intrinsic tumor-targeting capability and lack immunogenicity in vivo.

This multiplexed mass cytometry protocol uses thiol-reactive organoid barcoding in situ and a cytometry by time of flight signaling analysis pipeline (CyGNAL) to enable 126-plex single-cell analysis of cell type, cell state and post-translational modification signaling networks in organoids.

This protocol describes a proteomic approach for efficient affinity capture, identification and quantification of endogenous phosphoprotein phosphatases and associated proteins from cells and tissues.