We describe a protocol for imaging a mitochondrial fluorescence transient increase event (Mitoflash) in live cardiomyocytes using a confocal microscope. Mitoflash, detected by mitochondria-targeted circularly permuted fluorescent protein (mt-cpYFP), can be used to assess mitochondrial respiration function in situ. The protocol is also suitable for live-cell imaging of other adherent cells, including fibroblasts and hepatocytes. For complete details on the use and execution of this protocol, please refer to Gong et al. (2014) and Gong et al. (2015).Detailed study of cellular organelles requires their isolation. Several protocols have been described for the isolation of the Golgi apparatus from liver tissue, but these are not suitable and not reproducible in harder tissues. Here, we describe a protocol to isolate Golgi vesicles from cardiac tissue using a discontinuous sucrose gradient. For complete details on the use and execution of this protocol, please refer to Tarazon et al. (2017).Cellular traction forces influence epithelial behavior, including wound healing and cell extrusion. Here, we describe a simple in vitro traction force microscopy (TFM) protocol using ECM protein-coated polydimethylsiloxane substrate and widefield fluorescence microscopy. We include detailed steps for analysis so readers can obtain traction forces to study the mechanobiology of epithelial cells. We also provide guidelines on when to adopt another common class of TFM protocols based on polyacrylamide hydrogels. For complete details on the use and execution of this protocol, please refer to Saw et al. (2017) and Teo et al. (2020).The potential of reprogrammed β cells derived from pancreatic exocrine cells to treat diabetes has been demonstrated in animal models. However, the precise mechanisms and regulators involved in this process are not clear. Here, we describe a method that allows mechanistic studies of this process in primary exocrine cultures using adenoviral expression vectors. This rapid 5-day protocol, provides the researcher with a highly controlled experimental system in which the effects of different compounds or genetic manipulations can be studied. For complete details on the use and execution of this protocol, please refer to Elhanani et al. (2020).Clustering of synaptic vesicles along the neuronal axons is a critical mechanism underpinning proper synaptic transmission. Here, we provide a detailed protocol for analyzing the distribution of synaptic vesicles in presynaptic boutons of cultured neurons. The protocol covers preparation of cultured neurons, expression of synaptic vesicle-enriched proteins, and quantification procedures. Utilizing neurons from postnatal transgenic mice, this method can be applied to investigate the roles of synaptic genes in regulating vesicle dynamics at synaptic sites. For complete details on the use and execution of this protocol, please refer to Han et al. (2020a).Many studies in systems neuroscience use head-fixation preparations for in vivo experimentation. While head-fixation confers several advantages, one major limitation is the lack of behavioral measures that quantify whole-body movements. Here, we detail a step-by-step protocol for using a novel head-fixation device that measures the forces exerted by head-fixed mice in multiple dimensions. We further detail how this system can be used in conjunction with in vivo electrophysiology and optogenetics to study dopamine neurons in the ventral tegmental area. For complete details on the use and execution of this protocol, please refer to Hughes et al. (2020a, 2020b).Single cell RNA sequencing of human thymic cells is dependent on isolation of highly pure and viable cell populations. This protocol describes the isolation of CD34+ progenitor and more differentiated CD34- fractions from post-natal thymic tissue to study thymopoiesis. CD34+ cells represent less then 1% of thymic cells, so this protocol uses magnetic- followed by fluorescence-activated cell separation to isolate highly enriched CD34+ cells. For complete details on the use and execution of this protocol, please refer to Le et al. (2020).Healthy vaginal epithelium is essential for normal reproductive functions and protects against infectious diseases. Here, we present a protocol for developing mouse vaginal organoids from single epithelial cells. These organoids recapitulate both functional and structural characteristics of vagina in situ. This model is a powerful tool for investigating how vaginal microbiome or chemicals in contraceptives and personal hygiene products interact with stem cells and alter the epithelial dynamics, which will lead to new insights into the pathogenesis of vaginal diseases. For complete details on the use and execution of this protocol, please refer to Ali et al. (2020).We describe an ex vivo EGF ligand internalization assay using fresh patient tumor biopsies to determine how antigen targets will be trafficked before patients receive mAb treatment.  https://www.selleckchem.com/products/Erlotinib-Hydrochloride.html  This protocol facilitates a sensitive and reproducible indication as to mAbs surface retention times during treatment. EGF uptake protocols can also be used to analyze EGFR heterogeneity and localization of EGFR in both tumor and xenograft tissue. The technology can be adapted to analyze other receptors such as PD-L1 for which methods are provided. For complete details on the use and execution of this protocol, please refer to Joseph et al. (2019) and Chew et al. (2020).Primary hepatocytes are a vital tool in various biomedical research disciplines, serving as an ex vivo model for liver physiology. Obtaining high yields of viable primary mouse hepatocytes is technically challenging, limiting their use. Here, we present an improved protocol based on the classic two-step collagenase perfusion technique. The liver is washed by perfusion, hepatocytes are dissociated by collagenase, separated from other cells, and cultured. This protocol was optimized to significantly reduce procedure duration and improve hepatocyte yield and viability.Retention of multiplet captures in single-cell RNA sequencing (scRNA-seq) data can hinder identification of discrete or transitional cell populations and associated marker genes. To overcome this challenge, we created DoubletDecon to identify and remove doublets, multiplets of two cells, by using a combination of deconvolution to identify putative doublets and analyses of unique gene expression. Here, we provide the protocol for running DoubletDecon on scRNA-seq data. For complete details on the use and execution of this protocol, please refer to DePasquale et al. (2019).