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Studying human brain vascular cells with single-cell transcriptomics and organoids
Human brain vascular cells, including endothelial and mural cells, can be purified with FACS and used in many downstream applications, including cell culture, transcriptomics and organoid transplants. This image shows vascular cells labeled with GFP and transplanted on top of induced pluripotent stem cell (iPSC)-derived cortical organoids. See Crouch et al. p603
Image : Elizabeth Crouch, University of California San Francisco. Cover design: S. Whitham
This article describes the main sources of bias in small RNA-sequencing and the importance of obtaining structure-level information for the correct interpretation of high-throughput sequencing results.
A protocol extension describing the purification of prenatal human brain endothelial and mural cells with FACS and their utilization in downstream applications, including cell culture, organoid transplantation and single-cell transcriptomics.
Genome-scale metabolic models enable mathematical exploration of metabolism under various defined conditions. This protocol describes GECKO, a method for enhancing a genome-scale metabolic model with enzymatic constraints using kinetic and omics data (e.g., proteomics).
The authors describe a high-throughput screening strategy that can be carried out anaerobically for studying the effects of drugs in vitro on individual gut microbes or microbial communities created synthetically or obtained from stool samples.
This protocol presents a comprehensive workflow for the implementation of whole-genome sequencing in routine tumor diagnostics, exemplified by the pipeline used in the Netherlands Cancer Institute.
Antigen-specific B cells constitute a small proportion of the total B cell population, making identification for downstream analysis challenging. Here, this is achieved by pairing fluorescent antigen tetramer probes with a sensitive enrichment approach.
This protocol provides extensive guidelines and detailed steps to generate novel bio-engineered bacterial strains using CRISPR-associated transposase (CAST) systems, with available plasmids and standard molecular biology techniques.
Mapping of chromatin states at single-cell resolution is still challenging. This protocol describes nano-CT, a novel method to simultaneously characterize up to three epigenetic modalities at single-cell resolution.
The procedure guides inexperienced users interested in handling spatial omics data in a Python environment to streamline data analysis and to facilitate benchmarking analysis via the spatial omics database.
A protocol detailing the labeling and identification of cell- and subcompartment-specific proteins found within intact astrocytes and neurons in vivo using the proximity-dependent biotinylation system BioID2.
A customized hyperspectral confocal microscope enables the tracking of living cells and sensing of cellular processes by characterizing bio-integrated microlasers with high spectral resolution.
A protocol describing how to implant head-mounted jugular vein catheters in mice. This procedure facilitates systemic drug administration in a variety of experimental settings, including optical recording and manipulation of neuronal activities and behavioral tests.