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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.
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.
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 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.
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.
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 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.
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.
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.
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 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.
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.
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.
This protocol describes how to perform single-particle tracking photoactivated localization microscopy (sptPALM) of membrane proteins in living plant tissues. The procedure covers all stages, from sample preparation to data analysis.
The authors provide experimental and computational procedures, including details on building an automated fluidic exchange system, for high-resolution imaging of multiple transcripts and chromatin structure in fixed cells or cryosectioned tissue.
The authors present a protocol for producing cyclic peptide precursors in Pichia pastoris that undergo in vitro enzymatic maturation into cyclic peptides using recombinant asparaginyl endopeptidases. Assays for characterizing purified cyclic peptides are also described.
CRISPR-induced on-target effects (large deletions, large insertions, rearrangements or loss of heterozygosity) occur frequently at the edited site. This protocol describes how to identify these effects using quantitative genotyping PCR and SNP genotyping.