Volume 13 Issue 12, December 2018

In this tutorial, the authors provide a comprehensive description of the considerations for designing single-cell transcriptomics studies, from sample preparation and single-cell RNA sequencing methodologies through data processing and analysis.

Adult endothelial cells from mice are reprogrammed to hematopoietic stem cells without transitioning through a pluripotent state. The protocol also describes in vitro and in vivo assays to confirm that the resulting cells function as expected.

This computational protocol offers a framework to integrate high-dimensional -omics datasets. A three-pronged association study integrating intestinal microbiome and serum metabolome data with measures of human host physiology is used as an example.

Ciric et al. describe a protocol for the removal of motion artifacts from functional MRI data. They introduce a software package that implements common denoising protocols and provides tools for assessing the efficacy of denoising.

Endothelial cells, pericytes and astrocytes are cocultured to generate organoids that reproduce many features of the blood–brain barrier. This protocol also describes how to analyze drug penetration into the organoids.

This protocol provides approaches for applying the CRISPR–Cas9 system for genome editing in apple and grapevine plants, using both plasmid-mediated delivery of components and direct delivery of CRISPR–Cas9 ribonucleoproteins.

Valuable structural information can be derived by chemical cross-linking of proteins followed by mass spectrometry of the products. Iacobucci et al. use MS-cleavable reagents, enrichment by strong-cation-exchange chromatography, and LC-MS/MS analysis.

This protocol describes how to generate high-resolution maps of the elastic properties of biomolecules and polymers using bimodal AFM. The procedure covers sample preparation, bimodal AFM setup and calibration, and data acquisition and processing.

This protocol describes strategies for targeted genome modification in axolotls. Eggs are injected with a CAS9–gRNA ribonucleoprotein complex, which allows for efficient generation of knockout and knock-in animals and immediate phenotypic analysis.

This protocol describes procedures for speed-breeding approaches using growth cabinets and LED-supplemented glasshouses. The approaches can be used to accelerate crop research and are compatible with a wide variety of crops.

Cross-linking of amino acids in close proximity on protein surfaces, followed by mass spectrometry, provides useful structural information. This protocol for using XlinkX can be applied for analysis of cultured cell samples or purified complexes.

This protocol describes a suite of lentiviral transfer plasmids that can be used for high-yield, time- and cost-efficient, and constitutive or inducible production of soluble and membrane proteins in mammalian cell lines.

This protocol describes the differentiation of hiPSCs into cardiomyocytes and subsequent cytotoxicity and contractility assays needed to calculate the ‘cardiac safety index’, which models the likelihood that a drug is cardiotoxic.

3D image segmentation and strain mapping are applied to topologically complex structures. As an example, we present the resolution of 3D strains on a culture containing neurons, astrocytes, and neural progenitors undergoing an in vitro injury event.