Volume 15 Issue 3, March 2020

In this extension to their original protocol applying TAR cloning to mammalian genomes, the authors apply the technique to microbes and environmental DNA samples, by adding ARS-like elements not commonly found in microbial genomes to the TAR cloning vector.

This protocol describes a lentiviral tagging approach that permits sequential rounds of cell labeling and lineage reconstruction in cells amenable to viral transduction. Transcriptomes and CellTags are captured simultaneously on a droplet-based scRNA-seq platform.

This protocol describes the synthesis and applications of artificial antigen-presenting cell scaffolds. The scaffolds can be used for efficient ex vivo polyclonal T-cell expansion and antigen-specific enrichment of rare T-cell subpopulations.

This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data.

Cheap and non-toxic photocatalysts 9-fluorenone or rose bengal are used to oxidize non-activated alcohols or oxygenate tertiary amines, respectively, under irradiation from a blue light-emitting diode.

Here, the authors provide detailed experimental and analytical procedures for Hi-M, a method that enables simultaneous imaging of 3D genome folding and RNA localization in single cells.

This protocol describes how to establish an ovine critical-size, segmental bone defect model to study bone regeneration and reconstruction.

This protocol provides a set of seven customizable example procedures for using microcontroller boards (MCBs) and single-board computers (SBCs) for applications in chemical and biochemical research.

Fit-Hi-C is a computational tool for identifying statistically significant contacts from Hi-C data. This protocol describes how to apply the new version, called FitHiC2, on high-resolution Hi-C data, demonstrating the added functionalities.

This protocol describes the instrumentation and analysis methods needed to quantify particle dynamics during new particle formation of sub-3-nm aerosol particles in chamber experiments.

Infected lung is analyzed by two-photon imaging microscopy and can be observed for >4 h during the acute phase of inflammation and at for least 1 h in the lethal phase.

Various types of endothelial cells and CD157⁺ vascular-resident endothelial stem cells are isolated from mice by mechano-enzymatic tissue digestion followed by fluorescence-activated cell sorting.

This protocol enables isolation of viable and pure stem cell populations from muscle, and describes how to transplant the cells and follow repopulation and differentiation potential in vivo.

This protocol describes bioinformatics procedures to detect RNA editing in RNA-sequencing datasets using REDItools and REDIportal. REDItools is a software package to profile RNA editing, while known editing sites are collected in the REDIportal database.

This Protocol describes how to perform online buffer exchange (OBE) coupled to native mass spectrometry (nMS) for rapid screening of structural features of pre-purified proteins, protein complexes or clarified cell lysates.

This protocol describes how to anesthetize and image different organs of Drosophila larvae, including epidermis, gut, imaginal discs, neurons, fat body, tracheae, muscles and hemocytes. It also explains how to use laser ablation to probe cell properties.

Chromatin fibers are isolated from replicating tissues or cells and laid on glass slides. Labeled replicating DNA and chromatin-associated proteins are imaged by supperresolution microscopy, and their distribution on sister chromatids is quantified.

This protocol describes how to perform quantitative comparisons of protein-anchored chromatin contacts across experimental conditions by normalizing samples with spiked-in nuclei from an orthogonal species. This strategy can reveal global changes in chromatin interactions.

Mice are trained to use a custom-made robotic manipulandum to enable study of motor learning. The device can be used in conjunction with neurophysiological and microscopy techniques that require head fixation.

This protocol describes a suite of related approaches for genome-wide profiling of DNA replication dynamics in unperturbed or synchronized cells by measuring DNA copy-number changes using high-throughput sequencing.

This protocol presents an imaging system that uses high-resolution confocal microscopy with a fluorochrome-labeled avidin probe to visualize mast cell degranulation in single cells subjected to shRNA knockdown or CRISPR–Cas9 gene editing.