Volume 15 Issue 10, October 2020

Embryonic stem cells undergo CRISPR–Cas9-mediated editing and are then used to reconstitute forebrain regions in mouse chimeras via neural blastocyst complementation.

This protocol describes the MAC-tag approach, which combines affinity purification and biotinylation identification proximity labeling in a single tag. Binding proteins are identified by liquid chromatography–mass spectrometry, followed by visualization of protein localization using an online platform.

This protocol provides a detailed guide to metaproteomics data analysis and visualization. The modular and customizable workflow is based on two open-source tools (MetaProteomeAnalyzer and Prophane) and is illustrated with example datasets.

This protocol describes a comprehensive computational pipeline for reference-free deconvolution of bulk DNA methylation data, including data preprocessing, confounder adjustment, feature selection, and visualization and interpretation of the results.

The authors describe a streamlined epigenomic profiling protocol based on cut-and-paste tagmentation by the Tn5 transposase targeted to a chromatin protein of interest.

This protocol describes a toolbox for comprehensive characterization of inflammasome activation and cell death in response to both in vivo (in mice) and in vitro (using bone marrow–derived macrophages) models of infection, sterile insults, and cancer.

The authors describe detailed procedures for an epigenomic profiling method suitable for low-input samples that is based on in situ labeling with an oligonucleotide-conjugated antibody.

This protocol describes a combined approach for whole-mount fluorescence in situ hybridization (FISH) and immunofluorescence staining in zebrafish embryos and larvae.

This protocol summarizes the various approaches available to derive organoids from cancer patients and use these for screening of possible treatments. An optimized protocol for using head and neck cancer organoids is also described.

The authors describe a platform to screen arrays of designer epigenome modifiers (DEMs) targeting up to three genes of interest using a multicolor reporter cell line to determine combinations producing the most efficient epigenome editing.

This protocol describes how to isolate trophoblast from first-trimester human placentas and grow it long term in a three-dimensional organoid culture system.

The authors describe a standardized three-chamber social preference protocol that is sensitive and reliable at detecting social preference deficits in several mouse models of autism spectrum disorder.

This homology-directed insertion-based CRISPR gene-editing protocol enables knockout of all alleles of a target gene in the polyploid Drosophila S2R+ cell line, using either two sequential rounds of homology-directed insertion or a single round with a donor vector containing four different sgRNAs.

This protocol describes the synthesis of two fluorescent probes for (sub-)cellular detection of endogenous formaldehyde, including procedures for probe characterization and example applications in living cells and mouse tissue slices.

Solid acid catalysts are used in a wide variety of industrial catalytic processes for production of chemicals and petrochemicals. This protocol uses ³¹P NMR of phosphorous probes to characterize acidity in detail for both Brønsted and Lewis acid sites.