Protocol for isolating young adult parvalbumin interneurons from the mouse brain for extraction of high-quality RNA

Dysfunction in the parvalbumin (PV) subclass of GABAergic interneurons is implicated in several neurodevelopmental disorders that evolve in severity with postnatal developmental stages. Understanding the molecular underpinnings of the postnatal changes in the function of PV interneurons has been limited by the difficulty in the isolation of pure adult PV interneurons and high-quality RNA. Here, we describe our protocol for the isolation of pure young adult PV interneurons and preparation of high-quality RNA from these cells. For complete details on the use and execution of this protocol, please refer to Joseph et al. (2021).

Generation of hypoxia-sensing chimeric antigen receptor T cells

Exploiting hypoxia in solid malignancies to restrict expression of chimeric antigen receptors (CARs) on engineered T cells to the tumor microenvironment overcomes the risk of on-target off-tumor toxicity and minimizes tonic signaling, which promotes CAR T cell exhaustion. This protocol summarizes the synthetic biology underlying the development of a stringent oxygen-sensitive CAR for in vitro and in vivo preclinical characterization.

For complete details on the use and execution of this protocol, please refer to Kosti et al. (2021).

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Hypoxia can be exploited as a selective signal for tumor-specific CAR expression

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A protocol to enable stringent hypoxia-dependent CAR expression

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A dual oxygen-sensing expression system that is both dynamic and tunable

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An approach to provide a safety switch for non-tumor selective CAR targets

Murine cochlear cell sorting and cell-type-specific organoid culture

Neonatal mouse cochlear duct cells can proliferate and grow in vitro into inner ear organoids. Distinctive cochlear duct cell types have different organoid formation capacities. Here, we provide a flow cytometric cell-sorting method that allows the subsequent culture of individual cochlear cell populations. For the efficient culture of the sorted cells, we provide protocols for growing free-floating inner ear organoids, the adherence of organoids to a substrate, and the expansion of organoid-derived inner ear colonies.

For complete details on the use and execution of this protocol, please refer to Kubota et al. (2021).

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Flow cytometric sorting of mouse cochlear cells

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Culture of sorted cochlear cell populations and growth of inner ear organoids

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Adherent growth of inner ear organoid-derived colonies

Protocol for high-throughput compound screening using flow cytometry in THP-1 cells

Flow cytometry is a valuable method for analyzing protein expressions at the single cell level but can be difficult to apply to large numbers of samples. This protocol provides instructions to perform a high-throughput small molecule screen using flow cytometry analysis of THP-1 cells, a human monocytic leukemia cell line. We describe a methodology for identifying compounds that regulate PD-L1 surface expression in IFN-γ-stimulated cells, which has been successfully used to screen a collection of ∼200,000 compounds.

For complete details on the use and execution of this protocol, please refer to Zavareh et al. (2020).

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Protocol for high-throughput screening of compounds using flow cytometry

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Designed for quantification of cell surface expression of proteins in THP-1 cells

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This protocol has been used to identify modulators of PD-L1 expression

Protocol for the generation of murine bronchiolospheres

Organoid models have been shown to be valuable tools for studying epithelial-mesenchymal crosstalk during biological and pathological settings. Our data identified ACTA2+ PDGFRα+ repair-supportive mesenchymal cells as an important component of the conducting airway niche. Here, we provide a detailed protocol for culturing airway organoids, or bronchiolospheres, which provide an assessment of the ability of mesenchymal cells to support club-cell growth.

For complete details on the use and execution of this protocol, please refer to Moiseenko et al. (2020).

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Bronchiolospheres are a useful tool to model epithelial-mesenchymal interactions

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Different types of mesenchymal cells can be used to support club cell growth

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Cell differentiation within bronchiolospheres can be assessed after 16 days of culture

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Bronchiolospheres can be passaged multiple times

Protocol to establish a lung adenocarcinoma immunotherapy allograft mouse model with FACS and immunofluorescence-based analysis of tumor response

Anti-PD-1/PD-L1 therapy shows long-term effects in many cancer types, but resistance and relapse remain the main limitations of this therapy. Here, we describe a protocol to evaluate the tumor response to immunotherapy in a mouse lung cancer model. The protocol includes the establishment of the lung cancer mouse model, anti-PD-1 treatment, tumor-infiltrating lymphocyte isolation, immunofluorescence, and flow cytometry analysis. This protocol can also be applied to other cancer types and immunotherapies.

For complete details on the use and execution of this protocol, please refer to Yu et al. (2021)

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Establish a tumor-derived cell line from a genetic engineered lung cancer mouse model

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Evaluate the tumor response to immunotherapy using an allograft lung cancer model

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Isolate tumor-infiltrating lymphocytes from fresh tumor samples

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Evaluate activity of lymphocytes by flow cytometry and infiltration by immunofluorescence

Isolation of tumor-resident CD8+ T cells from human lung tumors

CD103⁺CD8⁺ tumor-resident memory T cells (T_RM) are important components of anti-tumor immunity. However, their role in response to cancer immunotherapy is not fully understood. The protocol describes how to isolate CD8⁺ T cells and autologous tumor cells from human lung tumors to study the functional activities of CD8⁺ T cells. Tumors are heterogeneous in terms of the quantity and quality of immune cell types, so the yield of T_RM cells depends on the features of the tumor. For complete details on the use and execution of this protocol, please refer to Corgnac et al. (2020).

Flow cytometry-based ex vivo murine NK cell cytotoxicity assay

Direct killing of diseased cells is a hallmark function of NK cells. This protocol describes a flow-based assay to measure in vivo activated murine NK cells’ ability to kill target cells ex vivo. Existing published protocols for assaying ex vivo NK cell killing utilized the radioactive chromium release assay or were designed for human NK cells. This protocol details specifically an ex vivo cytotoxicity assay using primary murine NK cells enriched from splenocytes that were activated in vivo with poly(I:C).

For complete details on the use and execution of this protocol, please refer to Wagner et al. (2020).

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This protocol describes a flow-based assay to assess mouse NK cell killing ex vivo

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Protocol details the procedure for enriching NK cells from mouse splenocytes

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In vivo poly(I:C) activated NK cells are used as effectors to kill labeled targets

Quantification of zinc intoxication of Candida glabrata after phagocytosis by primary macrophages

Zinc (Zn²⁺) is a trace element, playing pivotal roles during host-pathogen interactions. Macrophages can sequester Zn²⁺ and restrict bioavailability or increase phagolysosomal Zn²⁺ to kill pathogens. This method quantifies Zn²⁺-mediated clearance of the human fungal pathogen C. glabrata after phagocytosis by innate immune cells. Double staining with propidium iodide and a zinc-specific fluorescence dye allows for discrimination of live versus dead pathogens inside phagolysosomes. Moreover, elevated phagolysosomal Zn²⁺ decreases fungal viability as a function of intracellular Zn²⁺ concentrations in macrophages.

For complete details on the use and execution of this protocol, please refer to Riedelberger et al. (2020).

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A host-pathogen interaction system of primary macrophages and fungal pathogens

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Flow cytometric assay to quantify Zn²⁺ intoxication of fungal pathogens by macrophages

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Fungal viability depends on intra-phagosomal Zn²⁺ changes during immune responses

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Zn²⁺ levels in reisolated pathogens correlate with fungal killing by macrophages

Analysis of T cells in mouse lymphoid tissue and blood with flow cytometry

T cells play a key role in adaptive immunity. Defects in specific T cell receptors or signaling proteins can alter their frequency and activation status, which may be associated with immune disease or cancer. Monitoring of T cell frequency and function in genetically modified mice or murine models of disease is therefore of high interest. Here, we provide a detailed protocol to analyze regulatory T cells, T cell activation, and cytokine production in thymus, spleen, or blood via flow cytometry.

For complete details on the use and execution of this protocol, please refer to Demeyer et al. (2020).

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A protocol for the collection of blood, thymus, and spleen from mice

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Flow cytometry allows staining of different T cell populations

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Details for intracellular cytokine staining of T cells

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Full details for both flow cytometry panels and gating strategies

Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches

Significant advancements in understanding disease mechanisms can occur through combined analysis of next-generation sequencing datasets generated using purified cell populations. Here, we detail our optimized protocol for purification of mouse hepatic macrophages (or other liver non-parenchymal populations) suitable for use in various next-generation sequencing protocols. An alternative framework is described for sorting pre-fixed hepatic nuclei populations. This strategy has the advantage of rapidly preserving the nuclei and can facilitate success with ChIP-seq for more challenging molecules. For complete details on the use and execution of these protocols, please refer to Muse et al. (2018), Sakai et al. (2019), and Seidman et al. (2020).

In vitro differentiation of human embryonic stem cells to hemogenic endothelium and blood progenitors via embryoid body formation

Little is known about the emergence of blood progenitors during human embryogenesis due to ethical reasons and restricted embryo access. The use of human embryonic stem cells (hESCs) as a model system offers unique opportunities to dissect human blood cell formation. Here, we describe a protocol allowing the differentiation of hESCs via embryoid bodies toward hemogenic endothelium and its subsequent differentiation to blood progenitors. This protocol relies on the formation of embryoid bodies, which is tricky if not carefully performed. For complete details on the use and execution of this protocol, please refer to Garcia-Alegria et al. (2018).

Quantitative in vivo assessment of amyloid-beta phagocytic capacity in an Alzheimer's disease mouse model

Alzheimer's disease is characterized by the deposition of extracellular amyloid-beta (Aβ) plaques. While microglial phagocytosis is a major mechanism through which Aβ is cleared, there is no method for quantitatively assessing Aβ phagocytic capacity of microglia in vivo. Here, we present a flow cytometry-based method for investigating the Aβ phagocytic capacity of microglia in vivo. This method enables the direct comparison of Aβ phagocytic capacity between different microglial subpopulations as well as the direct isolation of Aβ phagocytic microglia for downstream applications. For complete details on the use and execution of this protocol, please refer to Lau et al. (2020).

Evaluating cytokine production by flow cytometry using brefeldin A in mice

Characterizing cytokine production in situ is important for properly understanding immunologic responses. Cytokine reporter mice are limited by the need to cross markers into various knockout backgrounds and by availability of reporters of interest. To overcome this, we utilize injection of brefeldin A into mice to enable flow cytometric analysis of in situ cytokine production during a bacterial infection. While we evaluate IFN-γ production during Burkholderia thailandensis infection, this protocol can be applied to other cytokines and other mouse models. For complete details on the use and execution of this protocol, please refer to Kovacs et al. (2020) and Liu and Whitton (2005).

Analysis of epicardial genes in embryonic mouse hearts with flow cytometry

Genetic markers used to define discrete cell populations are seldom expressed exclusively in the population of interest and are, thus, unsuitable when evaluated individually, especially in the absence of spatial and morphological information. Here, we present fluorescence in situ hybridization for flow cytometry to allow simultaneous analysis of multiple marker genes at the single whole-cell level, exemplified by application to the embryonic epicardium. The protocol facilitates multiplexed quantification of gene and protein expression and temporal changes across specific cell populations. For complete details on the use and execution of this protocol, please refer to Lupu et al. (2020).

Purification of micronuclei from cultured cells by flow cytometry

Micronuclei are aberrant nuclear compartments that form when chromosomes or chromosome fragments fail to incorporate into a primary nucleus during mitotic exit. Ruptures at the micronuclear envelope are associated with DNA damage and activation of immune sensing pathways. To gain insights into these processes, we have developed a method to purify ruptured micronuclei. This method paves the way toward understanding the consequences of micronuclear envelope rupture.

For complete details on the use and execution of this protocol, please refer to Mohr et al. (2021).

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An optimized protocol for purifying micronuclei with ruptured nuclear envelopes

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Use of fluorescent markers enables flow sorting of distinct populations of micronuclei

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Preservation of micronuclear protein and DNA content for functional characterization

Generation of TCRα-transduced T cells for adoptive transfer therapy of salmonellosis in mice

Adoptive transfer therapy has great potential to treat diseases such as cancer as well as autoimmune and infectious diseases. Identification of chain-centric T cell receptors (TCRs) with the dominant-active antigen-specific α-chains (TCRα) can significantly improve the efficacy of adoptive cell therapy while reducing time, labor, and costs of generation of TCR-modified antigen-specific T cells. This protocol describes how to generate salmonella-specific TCRα-modified mouse T cells by retroviral transduction and evaluate their functional activity in vivo in the mouse model of salmonellosis.

For complete details on the use and execution of this protocol, please refer to Kalinina et al. (2020).

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Adoptive T cell therapy has great potential for treatment of infections

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Protocol describes generating T cells transduced with dominant pathogen-specific TCRα

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Protocol describes usage of specific TCRα-transduced T cells in mice salmonellosis

In vitro and ex vivo evaluation of tumor-derived exosome-induced dendritic cell dysfunction in mouse

Exosomes that contain various signaling molecules, such as proteins, nucleotides, metabolites, and lipids, are important for intercellular communication. Dendritic cells (DC) are central regulators of anti-tumor immunity but can be suppressed by tumor-derived exosomes (TDEs) in the tumor microenvironment. Here, we describe a step-by-step protocol for TDE isolation and evaluation of TDEs on DCs both in vitro and ex vivo with high repeatability. This approach is useful for the interrogating TDE-DC interactions and identification of novel immune regulators. For complete details on the use and execution of this protocol, please refer to Yin et al. (2020).

Isolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis

The combination of population and single-cell RNA sequencing analysis using human embryonic stem cell (hESC) differentiation and developmental tissues is a powerful approach to elucidate an organ-specific cellular and molecular atlas in human embryogenesis. This protocol describes (1) cardiac-directed differentiation and isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting, (2) isolation of human embryonic heart-derived single cardiac cells, and (3) construction of cDNA libraries with Smart-seq2. These allow for the preparation of human developmental samples for comprehensive transcriptional analysis.

For complete details on the use and execution of this protocol, please refer to Sahara et al. (2019).

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Efficient cardiac-directed differentiation of hESCs

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Isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting

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Isolation of human embryonic heart-derived single cardiac cells

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Construction of cDNA libraries for both population and single-cell RNA sequencing

Protocol for human placental mesenchymal stem cell therapy in a murine model of intra-abdominal infection of hypervirulent Klebsiella

Hypervirulent Klebsiella pneumoniae (hvKP) strains cause extra-pulmonary infections such as intra-abdominal infection (IAI) even in healthy individuals due to its resistance to polymorphonuclear neutrophil (PMN) killing and a high incidence of multidrug resistance. To assess whether human placental mesenchymal stem cell (PMSC) therapy can be an effective treatment option, we established a murine model of hvKP-IAI to evaluate immune cell modulation and bacterial clearance for this highly lethal infection. This protocol can rapidly assess potential therapies for severe bacterial IAIs.

For complete details on the use and execution of this protocol, please refer to Wang et al. (2020).

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PMSC treatment in a mouse model of hvKP-induced intra-abdominal infection

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Isolation of mouse peritoneal immune cells without affixing mice to a dissecting board

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Analysis of PMN, T, and NK cells in peritoneal washings

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Determination of bacterial CFUs in hvKP-infected peritoneal fluid

Isolation and characterization of circulating pro-vascular progenitor cell subsets from human whole blood samples

The examination of circulating pro-vascular progenitor cell frequency and function is integral in understanding aberrant blood vessel homeostasis in individuals with cardiometabolic disease. Here, we outline the characterization of progenitor cell subsets from peripheral blood using high aldehyde dehydrogenase (ALDH) activity, an intracellular detoxification enzyme previously associated with pro-vascular progenitor cell status. Using this protocol, cells can be examined by flow cytometry for ALDH activity and lineage restricted cell surface markers simultaneously.

For complete details on the use and execution of this protocol, please refer to Terenzi et al. (2019) and Hess et al. (2019, 2020).

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Aldehyde dehydrogenase is superior in the isolation of progenitor cells

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Flow cytometry is an effective method to characterize pro-vascular cells

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Aggressive gating strategies allows for in-depth progenitor cell characterization

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The use of fresh blood samples will yield most accurate cell prevalence

Purification and preservation of satellite cells from human skeletal muscle

Regeneration and repair of skeletal muscle is driven by tissue-specific progenitor cells called satellite cells, which occupy a minority of the cells in the muscle. This protocol provides researchers with techniques to efficiently isolate and purify functional satellite cells from human muscle tissue. The proven techniques described here enable the preparation of purified and minimally altered satellite cells for in vitro and in vivo experimentation and for potential clinical applications.

For complete details on the use and execution of this protocol, please refer to Barruet et al. (2020) and Garcia et al. (2018).

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Techniques are described for efficient isolation of human satellite cells

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Quiescent and activated satellite cells are purified using surface markers

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Purification involves minimal alteration compared to culture or activation

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Purified satellite cells faithfully represent the natural state for applications

Isolation of spermatogenic cells from the cynomolgus macaque testis with flow cytometry

Here, we describe a detailed protocol for the isolation of purified populations of viable spermatogenic cells derived from the non-human primate model organism Macaca fascicularis (cynomolgus). Using fluorescence-activated cell sorting (FACS), we describe methods to isolate spermatogonia and primary spermatocytes ranging across the sub-stages of meiosis prophase I. These cell populations can be used with a variety of downstream assays, including single-cell approaches such as RNA sequencing, chromatin immunoprecipitation, quantitative RT-PCR, and immunocytochemistry. For complete details on the use and execution of this protocol, please refer to Lau et al. (2020).

Isolation of exophers from cardiomyocyte-reporter mouse strains by fluorescence-activated cell sorting

Cardiac exophers are membrane-bound extracellular vesicles released by cardiomyocytes with varied content and an average diameter of 3.5 μm. Here, we provide a detailed protocol to enable the identification and purification of cardiomyocyte-derived exophers by using fluorescence-activated cell sorting for downstream cellular and molecular analysis. This protocol requires the use of mouse strains expressing fluorescent proteins in cardiomyocytes.

For complete details on the use and execution of this protocol, please refer to Nicolás-Ávila et al. (2020).

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Optimized protocol for exopher isolation from cardiomyocytes using FACS

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Isolated exophers are suitable for downstream cellular and molecular analysis

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Includes sample preparation and gating strategy for exopher identification

FACS protocol for direct comparison of cell populations isolated from mice

A FACS protocol is described that eliminates isolation and staining artifacts to allow accurate comparison between cell populations isolated from organs obtained from disparate mouse groups. This protocol was validated by characterizing the estrogen receptor positive cells within the mammary gland of transgenic mice with different genotypes at different stages of the estrous cycle. We include protocols necessary to batch stage animals within the cycle to proceed directly to FACS, which provides optimal RNA yields for RNA-seq. For complete details on the use and execution of this protocol, please refer to Ludwik et al. (2020).

Enriching for human acute myeloid leukemia stem cells using reactive oxygen species-based cell sorting

Isolation of leukemia stem cells presents a challenge due to the heterogeneity of the immunophenotypic markers commonly used to identify blood stem cells. Several studies have reported that relative levels of reactive oxygen species (ROS) can be used to enrich for stem cell populations, suggesting a potential alternative to surface antigen-based methods. Here, we describe a protocol to enrich for stem cells from human acute myeloid leukemia specimens using relative levels of ROS. This protocol provides consistent enrichment of leukemia stem cells. For complete details on the use and execution of this protocol, please refer to Lagadinou et al. (2013) and Pei et al. (2018).

Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19

In December 2019, a new coronavirus, SARS-CoV-2, which causes the respiratory illness that led to the COVID-19 pandemic, was reported. In the face of such a new pathogen, special precautions must be taken to examine potentially infectious materials due to the lack of knowledge on disease transmissibility, infectivity, and molecular pathogenicity. Here, we present a complete and safe workflow for performing scRNA-seq experiments on blood samples of infected patients from cell isolation to data analysis using the micro-well based BD Rhapsody platform. For complete information on the use and execution of this protocol, please refer to Schulte-Schrepping et al. (2020).