Volume 16 Issue 4, April 2021

This protocol describes how to direct differentiation of human pluripotent stem cells in a 3D matrix of collagen I to cultures containing mature alveolar type II and I cells plus airway basal, ciliated, club and neuroendocrine cells.

This Protocol Extension details the use of zebrafish larvae as a simple and robust in vivo system for studying human norovirus infection, enabling evaluation of the antiviral effects and toxicities of small molecules.

Here, we present a protocol for high-throughput screening of SPOT-peptide arrays to assess the antibiofilm, antimicrobial and immunomodulatory activities of synthetic peptides.

Precise knowledge of the structure of metals supported and stabilized by zeolite frameworks informs improved design and synthesis of the catalysts. This tutorial describes scanning transmission electron microscopy approaches for their structural analysis.

We present a protocol for long-term intravital imaging of mouse mammary tissue while maintaining tissue access using a skin flap and an imaging chamber. Strategies are provided for single-cell imaging, photomanipulation and multiplexed analysis.

Dekkers et al. provide a toolbox for the long-term culture, genetic manipulation and xenotransplantation of human normal and breast cancer organoids.

A standardized protocol and data workflow for high-throughput analysis of the maternal serum metabolome is outlined. It uses multisegment injection–capillary electrophoresis–mass spectrometry and is applied to a multi-ethnic cohort of pregnant women.

The dynamics of cardiomyocyte cell cycle activity and proliferation in humans are poorly understood. This protocol describes how to measure cell division in infant hearts by multi-isotope imaging spectrometry after incorporation of ¹⁵N-thymidine.

Clevers et al. describe the establishment of tubuloid cultures from tissue and urine, as well as the generation and characterization of tubuloid cell–derived 3D tubular structures in a perfused microfluidic multi-chip platform.

The authors present a protocol for isolating and studying human gut-associated lymphoid tissue.

In this cooling system for soft robotics, finger-like actuators from smart gels have embedded micropores that dilate and contract in response to temperature. Internal hydraulic fluid flows through dilated pores, absorbs heat and vaporizes.

This protocol details a developmental barcoding system, using MARC1 mice and homing CRISPR, to generate hundreds of mutant alleles that can reveal information about each cell’s lineage.

In spooling electrochemiluminescence spectroscopy, light emission spectra are continuously recorded during an electrochemical sweep. The formation of luminescent intermediates and products is shown as a function of electrical potential.

This protocol combines nascent DNA labeling, hairpin adapter ligation and bisulfite sequencing to simultaneously measure the methylation state of parent and daughter strands of replicating DNA, permitting assessment of maintenance and de novo methylation.

This protocol describes how to integrate organoids into a vascularized organ-on-a-chip biofabricated platform. The platform is assembled in a 96-well format and allows the connection of two tissues through a single endothelialized microchannel blood vessel.

This protocol describes a flexible workflow for processing and analyzing cyclobutane pyrimidine dimer sequencing data to detect UV-induced DNA lesions across the human or yeast genome.

Human induced pluripotent stem cells are differentiated to the three main cell types found in the heart—cardiomyocytes, cardiac fibroblasts and cardiac endothelial cells—and then combined to form 3D cardiac microtissues.

The capture Hi-C assay and its variants require specialized statistical methods for identification of high-confidence contacts. This protocol presents a versatile computational pipeline for detecting interactions and performing downstream analyses.

The N4-acetylcytidine RNA modification is conserved in all domains of life. Here, the authors provide a detailed protocol for whole-transcriptome quantitative nucleotide resolution mapping of this modified nucleobase in different organisms.

The construction and processing of human brain tissue microarrays are described. The location of either proteins, using immunohistochemistry, or mRNA, using in situ hybridization, can be determined simultaneously in a large number of samples.