Published in STAR protocols
Hypoxia is known to stimulate mitochondrial reactive oxygen species (mROS) in cells. Here, we present a detailed protocol to detect mROS using MitoSOX staining in live cells under normoxia and hypoxia. Flow cytometry allows sensitive and reliable quantification of mROS by FlowJo software. We optimized several aspects of the procedure including hypo...
Published in STAR protocols
As a key industrial nitrogenous product and a critical environmental pollutant, ammonia broadly affects our daily lives. Rapid and sensitive detection of ammonia is essential to both environmental monitoring and process control for industrial manufacturing. Here, we present a protocol for rapid detection of low amounts of ammonia in the aqueous pha...
Published in STAR protocols
For decades, the fruit fly Drosophila melanogaster has been an efficient genetic model to investigate many aspects of human neurodegenerative diseases. Through genetic and pharmacologic approaches, these studies have revealed the molecular mechanisms underlying disease pathogenesis and provided therapeutic implications. Here, we describe a protocol...
Published in STAR protocols
This protocol describes the production of hepatocyte-like cells (HLCs) from human pluripotent stem cells and how to induce hepatic steatosis, a condition characterized by intracellular lipid accumulation. Following differentiation to an HLC phenotype, intracellular lipid accumulation is induced with a steatosis induction cocktail, allowing the user...
Published in STAR protocols
Recently, it has become evident that macrophage diversity increases in the liver during the pathogenesis of non-alcoholic steatohepatitis (NASH). Here, we provide a detailed protocol for the analysis of liver macrophage subsets in mice with non-alcoholic fatty liver disease (NAFLD) and early NASH using flow cytometry and immunofluorescence (IF). Th...
Published in STAR protocols
Identification of peptides mediating protein-protein interaction (PPI) is crucial for understanding the function of interlinked proteins in cellular processes and amino acid-associated diseases. Traditional PPI assays are laborious, involving the generation of many truncated proteins. SPOT peptide assay allows high-throughput detection of domains e...
Published in STAR protocols
The jugular-nodose ganglia contain the sensory peripheral neurons of the vagus nerve, linking visceral organs to the medulla oblongata. Accessing these ganglia in smaller animals without damaging the vascular and neural structures may be challenging, as ganglionic fibers imbed deeply into the carotid sheath, and vagal parasympathetic fibers cross t...
Published in STAR protocols
Here, we describe a high-throughput 3D differentiation protocol for deriving midbrain dopaminergic neurons from human pluripotent stem cells. The use of organoids has become prevalent in disease modeling, but there is a high demand for more homogeneous cultures. Our approach is advantageous for large-scale production of uniform midbrain organoids t...
Published in STAR protocols
Single-cell RNA sequencing (scRNA-seq) provides the transcriptome of individual cells and addresses previously intractable problems including the central nervous system's transcriptional responses during health and disease. However, dissociating brain cells is challenging and induces artificial transcriptional responses. Here, we describe an enzyma...
Published in STAR protocols
The ascorbate peroxidase APEX2 is commonly used to study the neighborhood of a protein of interest by proximity-dependent biotinylation. Here, we describe a protocol for sample processing compatible with immunoblotting and mass spectrometry, suitable to specifically map the content of autophagosomes and potentially other short-lived endomembrane tr...
