Volume 16 Issue 8, August 2021

The authors present a protocol for testing physiologically relevant infection conditions (e.g., lung and wound exudate or blood) in minimal inhibitory concentration (MIC) assays.

This protocol describes FlowSOM, a clustering and visualization algorithm for unsupervised analysis of high-dimensional cytometry data. The protocol provides clearly annotated R code and an example dataset for inexperienced users.

This protocol describes co-detection by indexing, a highly multiplexed imaging technology that uses DNA-conjugated antibodies to image up to 60 markers in formalin-fixed, paraffin-embedded and fresh-frozen tissues.

This protocol provides a step-by-step workflow for prioritizing the cell types most responsive to an experimental perturbation in single-cell data and describes various applications of the pipeline in five case studies.

The protocol describes coculture of a primary human colon monolayer derived from cells growing in colon organoids with aerotolerant bacteria, such as strains of B. thetaiotaomicron genetically engineered to respond to different stimuli in colonic microenviroments.

This protocol describes the setup and characterization of a supramolecular assembly of small precursors into colloids or fibers driven by carbodiimide fuels. When the fuel is spent, the reaction reverses to form the initial peptides or amino acids.

This protocol sets up a bioluminescent repair reporter system using engineered Gaussia and Vargula luciferases for noninvasive tracking of homology-directed repair and nonhomologous end joining, respectively, induced by SceI meganuclease, SpCas9 or SpCas9 D10A nickase-mediated editing.

The authors provide a protocol for generating mouse–human chimeric embryos by injecting naive human pluripotent stem cells converted from the primed state.

The protocol describes a quantitative measurement that uses commercially available reagents to compare thrombogenic products against the World Health Organization standard for factor XIa procoagulant activity.

This is a protocol for profiling the methylome and transcriptome of a single cell by using Smart-seq2 and reduced representation bisulfite sequencing.

This protocol provides step-by-step instructions for using MetaNeighbor, a computational tool that allows quantification of cell-type replicability across single-cell transcriptomic datasets and identifies the gene sets that contribute to cell identity.

The glomerulus is a difficult-to-isolate structure that is often poorly represented in single-cell kidney preparations. This protocol describes the isolation of high-quality mouse glomerular cells for high-throughput analyses.

This protocol describes a plate-based ATAC-seq assay that combines up-front bulk tagging of accessible DNA by the Tn5 transposase with FACS sorting for robust and cost-efficient profiling of chromatin accessibility in single cells.