76
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Madhukaran S, Hon GC, Mahendroo M. Protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. STAR Protoc 2023; 4:102631. [PMID: 37897730 PMCID: PMC10751548 DOI: 10.1016/j.xpro.2023.102631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/24/2023] [Accepted: 09/20/2023] [Indexed: 10/30/2023] Open
Abstract
A challenge in studying cervical epithelial cell biology at the single-cell level is that differentiated subtypes, in particular mucus-secreting goblet cells, are sensitive to disassociating enzymes making isolation of all epithelial subpopulations difficult. Here we present a protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing. We describe steps for harvesting cervices, preparing cervical tissue, dissociation of cervical cells, and viability checks. We then detail library preparation, sequencing, and procedure for data analysis. For complete details on the use and execution of this protocol, please refer to Cooley et al. (2023).1.
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77
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Bafna A, Lau P, Banks G, Nolan PM. Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis. STAR Protoc 2023; 4:102618. [PMID: 37756154 PMCID: PMC10539961 DOI: 10.1016/j.xpro.2023.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The mammalian suprachiasmatic nucleus (SCN) is the principal circadian clock that synchronizes daily behavioral and physiological responses in response to environmental cues. Here, we present a protocol for harvesting mouse SCN by vibrating microtome for diurnal transcriptome analysis. We describe steps for mouse entrainment, isolation of the SCN, tissue preparation, slicing with a vibratome, and handling of the harvested SCN for RNA extraction. This protocol can also be used for harvesting other mammalian brain regions for genomic studies.
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78
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Hageter J, Starkey J, Barr A, Huff JR, Horstick EJ. Protocol for controlling visual experience during zebrafish development and modulation of motor behavior. STAR Protoc 2023; 4:102636. [PMID: 37837624 PMCID: PMC10589883 DOI: 10.1016/j.xpro.2023.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/16/2023] Open
Abstract
Sensory experience instructs neurodevelopment and refines sensory processing. Here, we describe a minimally invasive protocol to immobilize zebrafish during early development to control visual experience. We describe how to prepare larvae for embedding in agarose at two separate timepoints in development. Then we describe how to build a behavior rig and use software to track zebrafish behaviors. Finally, we detail analyzing behavioral data to validate the protocol and determine outcomes of sensory dependent plasticity. For complete details on the use and execution of this protocol, please refer to Hageter et al. (2023).1.
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79
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Kiparaki M, Baker NE. Protocol for assessing translation in living Drosophila imaginal discs by O-propargyl-puromycin incorporation. STAR Protoc 2023; 4:102653. [PMID: 37862174 PMCID: PMC10616417 DOI: 10.1016/j.xpro.2023.102653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/22/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023] Open
Abstract
Translation is a fundamental process of cellular behavior. Here, we present a protocol for measuring translation in Drosophila epithelial tissues using O-propargyl-puromycin (OPP), a puromycin derivative. We detail steps for larval dissection, OPP incorporation, fixation, OPP labeling, immunostaining, and imaging. We also provide details of quantification analysis. Significantly, OPP addition to methionine-containing media enables polypeptide labeling in living cells. Here, we study wing imaginal discs, an excellent model system for investigating growth, proliferation, pattern formation, differentiation, and cell death. For complete details on the use and execution of this protocol, please refer to Lee et al. (2018), Ji et al. (2019), and Kiparaki et al. (2022).1,2,3.
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80
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Harusato A, Seo W, Abo H, Nakanishi Y, Nishikawa H, Itoh Y. Protocol for acquiring samples to assess the impact of microplastics on immune microenvironments in the mouse intestine. STAR Protoc 2023; 4:102648. [PMID: 37865913 PMCID: PMC10598693 DOI: 10.1016/j.xpro.2023.102648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023] Open
Abstract
Environmental nano- and microplastics (NMPs) pose serious environmental issues, yet there is no established technique to assess their impact on health through oral ingestion. Here, we present a protocol to assess the impact of NMPs in the intestinal immune microenvironments by employing chronic exposure to NMPs in a mouse model. We describe steps for administration of NMPs, feces and tissue collection, and colonic gut digestion. We then detail procedures for isolation of intestinal immune cells and RNA isolation. For complete details on the use and execution of this protocol, please refer to Harusato et al.1.
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81
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Bearce EA, Ricamona BTB, Fisher KH, O'Hara-Smith JR, Grimes DT. Visualization and quantitation of spine deformity in zebrafish models of scoliosis by micro-computed tomography. STAR Protoc 2023; 4:102739. [PMID: 38043059 PMCID: PMC10775897 DOI: 10.1016/j.xpro.2023.102739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/26/2023] [Accepted: 11/07/2023] [Indexed: 12/05/2023] Open
Abstract
Zebrafish (Danio rerio) are increasingly used to investigate spine development, growth, and for studying the etiology of spinal deformity, such as scoliosis. Here, we present a micro-computed tomography-based pipeline for visualizing the zebrafish skeleton. We describe steps for sample preparation, imaging, data management, and processing. We then detail analysis of vertebral and spine morphology using open-source software. This protocol will be useful for scientists using zebrafish to understand spine development and disease. For complete details on the use and execution of this protocol, please refer to Bearce et al. (2022).1.
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82
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Decker-Farrell AR, Ma A, Li F, Muir A, Olive KP. Generation and ex vivo culture of murine and human pancreatic ductal adenocarcinoma tissue slice explants. STAR Protoc 2023; 4:102711. [PMID: 37950862 PMCID: PMC10682255 DOI: 10.1016/j.xpro.2023.102711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/14/2023] [Accepted: 10/23/2023] [Indexed: 11/13/2023] Open
Abstract
Traditional 2D/3D co-culture models typically do not reflect the cellular heterogeneity of pancreatic ductal adenocarcinoma (PDAC) tumors, while in vivo models can be slow and ill-suited to mechanistic investigations. Here, we present a protocol for culturing murine PDAC explants and a corresponding human PDAC model using tissue slice explants. We describe steps for sponge production, preparation of media and materials, tissue collection, and sectioning. We then detail procedures for explant plating, daily culture, and collection of samples.
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83
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Li L, Xu B, Liu C. Sample enrichment for single-nucleus sequencing using concanavalin A-conjugated magnetic beads. STAR Protoc 2023; 4:102595. [PMID: 37740915 PMCID: PMC10520929 DOI: 10.1016/j.xpro.2023.102595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 09/01/2023] [Indexed: 09/25/2023] Open
Abstract
Single-cell/nucleus sequencing has been increasingly used to study specific cell populations. However, cells/nuclei often become diluted during isolation steps and are difficult to reconcentrate through centrifugation. Here, we present a protocol for sample enrichment using concanavalin A-conjugated magnetic beads. We describe steps for dissection, nuclei isolation, and fluorescence-activated cell sorting (FACS). We then detail procedures for nuclei enrichment and library preparation. This protocol enables efficient retrieval and enrichment of cells/nuclei following FACS and integrates into existing workflows of various 10× Genomics applications.
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84
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Kolhe JA, Babu NL, Freeman BC. Protocol for establishing a protein interactome based on close physical proximity to a target protein within live budding yeast. STAR Protoc 2023; 4:102663. [PMID: 37883222 PMCID: PMC10630676 DOI: 10.1016/j.xpro.2023.102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/28/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
Here, we present a protocol for establishing a protein interactome based on close physical proximity to a target protein within live yeast cells. We describe steps for capturing both transient and stable binders by integrating a non-natural amino acid. We detail procedures for employing a site-directed method for labeling the surface that mediates protein associations and uncovers the binding sites on the interactors. Combined with mass spectrometry, our approach proves valuable in discovering binding partners and constructing a comprehensive protein-interaction network.
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85
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Pineda-Santaella A, Martín-García R, Fernández-Álvarez A. Analyzing self-assembled spindle dynamics in fission yeast meiosis using in vivo fluorescence imaging. STAR Protoc 2023; 4:102655. [PMID: 37864786 PMCID: PMC10598709 DOI: 10.1016/j.xpro.2023.102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/21/2023] [Accepted: 09/29/2023] [Indexed: 10/23/2023] Open
Abstract
Chromosome segregation in female meiosis in many metazoans is mediated by acentrosomal spindles. The analysis of the dynamics of self-assembled spindles is a challenge due to the low availability of oocytes. Here, we present a protocol for analyzing self-assembled spindle dynamics in fission yeast meiosis using in vivo fluorescence imaging. We describe steps for starter culture preparation, meiosis induction, and sample preparation. We then detail procedures for acquisition and analysis of images of self-assembled spindles. For complete details on the use and execution of this protocol, please refer to Pineda-Santaella and Fernández-Álvarez (2019)1 and Pineda-Santaella et al. (2021).2.
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86
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Rawat A, Jha MK, Morrison BM. Adoptive cell transfer of macrophages following peripheral nerve injury in mice. STAR Protoc 2023; 4:102624. [PMID: 37995193 PMCID: PMC10687290 DOI: 10.1016/j.xpro.2023.102624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/29/2023] [Accepted: 09/15/2023] [Indexed: 11/25/2023] Open
Abstract
Macrophages are key innate immune cells involved in multiple biological processes, including peripheral nerve regeneration. Here, we describe a protocol for the adoptive cell transfer of bone-marrow-derived macrophages (BMDMs) following sciatic nerve crush injury (SNCI). This procedure involves isolating BMDMs from a donor mouse, potentially manipulating them ex vivo, and reintroducing them into an animal following SNCI. Preclinical studies show that BMDMs can infiltrate injured nerves and impact functional recovery, potentially providing a novel therapy for nerve injuries. For complete details on the use and execution of this protocol, please refer to Jha et al.1.
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87
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Johnson CE, Williams E, Dewan A. Protocol for quantifying the odor detection threshold of mice. STAR Protoc 2023; 4:102635. [PMID: 37805920 PMCID: PMC10579531 DOI: 10.1016/j.xpro.2023.102635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/02/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
Perceptual measures of odor threshold provide a mechanism to compare sensitivity across species and to gauge stimulus concentrations for functional experiments. Here, we present a protocol to precisely quantify the odor detection threshold of mice. We describe the construction of a head-fixed operant conditioning behavioral rig and provide details of the training and testing procedures. This approach can be used to compare the sensitivity of mice across odorants and to quantify detection differences associated with genetic mutations or pharmacological manipulations. For complete details on the use and execution of this protocol, please refer to Johnson et al. (2023),1 Jennings et al. (2022),2 Williams and Dewan (2020),3 and Dewan et al. (2018).4.
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88
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Pitre Z, Seltzer T, Kalthoff C, Benitez-Cortez M, Yee C, Glennon EKK, Primavera VI, Kaushansky A. Protocol for assembling and implementing a partially automated system for rearing and handling Anopheles stephensi mosquitoes. STAR Protoc 2023; 4:102621. [PMID: 37776521 PMCID: PMC10558827 DOI: 10.1016/j.xpro.2023.102621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/03/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Live mosquitoes are required to comprehensively study vector-borne diseases, including transmission. Traditional mosquito-rearing protocols are laborious and time consuming. Here, we present a protocol for assembling and implementing a partially automated system for rearing and handling Anopheles stephensi mosquitoes. We describe steps for assembling a pupation station, self-emptying bucket, pupal funnel and dish vacuum, automatic aspirator, and sugar tubes. We also detail the application of these systems, along with specific limitations.
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89
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Terstege DJ, Dawson M, Jamani NF, Tsutsui M, Epp JR, Sargin D. Protocol for the integration of fiber photometry and social behavior in rodent models. STAR Protoc 2023; 4:102689. [PMID: 37979176 PMCID: PMC10694594 DOI: 10.1016/j.xpro.2023.102689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/20/2023] Open
Abstract
Fiber photometry offers insight into cell-type-specific activity underlying social interactions. We provide a protocol for the integration of fiber photometry recordings into the analysis of social behavior in rodent models. This includes considerations during surgery, notes on synchronizing fiber photometry with behavioral recordings, advice on using multi-animal behavioral tracking software, and scripts for the analysis of fiber photometry recordings. For complete details on the use and execution of this protocol, please refer to Dawson et al. (2023).1.
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90
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Mu C, Shearer J. Protocol for measuring respiratory function of mitochondria in frozen colon tissue from rats. STAR Protoc 2023; 4:102560. [PMID: 37742174 PMCID: PMC10522993 DOI: 10.1016/j.xpro.2023.102560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Mitochondrial respirometry allows for the comprehensive study of oxygen consumption within the electron transport system in tissues. However, limited techniques exist for analyzing frozen or biobanked intestinal tissues. Here, we present a protocol to evaluate the respiratory function of mitochondria in colonic tissues after cryopreservation at -80°C. We describe steps for rat dissection, respirometry calibration, and tissue preparation. We then detail measurement of oxygen respiration and protein concentration. This protocol facilitates the retrospective analysis of mitochondrial respiration in frozen tissue.
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91
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Guo J, Ying F, Cai J, Wang Z. A protocol for selection in mice of highly metastatic ovarian cancer cell with omental tropism. STAR Protoc 2023; 4:102642. [PMID: 37924519 PMCID: PMC10656258 DOI: 10.1016/j.xpro.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/23/2023] [Accepted: 09/25/2023] [Indexed: 11/06/2023] Open
Abstract
Preclinical models mimicking spontaneous omental metastasis from ovarian cancer (OC) can benefit the study of anti-metastatic therapies for OC patients. Here, we present a protocol to establish a highly metastatic (HM) mouse model with omental tropism by in vivo selection. We describe the processes of implanting OC cells in the ovaries of mice and obtaining HM sublines from their omental metastases. HM cells can metastasize from the ovary to the omentum within 2 weeks. For complete details on the use and execution of this protocol, please refer to Ying et al.1.
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92
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Wang R, Velentzas PD, Baehrecke EH. Mass isolation of staged Drosophila pupal intestines for analysis of protein ubiquitylation. STAR Protoc 2023; 4:102713. [PMID: 37950865 PMCID: PMC10682243 DOI: 10.1016/j.xpro.2023.102713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023] Open
Abstract
Large quantities of developmentally synchronized pupal intestines are required for biochemistry experiments. Here, we present a protocol for the mass isolation of staged pupal intestines during Drosophila melanogaster development based on buoyancy in sucrose for biochemical evaluation of protein ubiquitylation. We describe steps for crossing flies, preparation of samples, immunoprecipitation of proteins from staged isolated tissues, and analysis of samples by western blot. This protocol can be extended to investigate biochemical changes in other tissues. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).1.
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93
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Gopal A, Ibrahim R, Karsan A. Protocol for performing consecutive bone marrow transplants in mice to study the role of marrow niche in supporting hematopoiesis. STAR Protoc 2023; 4:102719. [PMID: 37967015 PMCID: PMC10684876 DOI: 10.1016/j.xpro.2023.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023] Open
Abstract
Hematopoietic stem and progenitor cells depend on bone marrow (BM) stromal cells for survival. Here, we present a protocol for performing three consecutive BM transplants in mice to study the role of BM niche in supporting hematopoiesis. We describe steps for transplanting cells to condition the marrow of the recipient mice and transplanting wild-type cells to examine the effect of the conditioned marrow in supporting hematopoiesis. We then detail procedures for transplanting into wild-type recipients to measure bone marrow chimerism. For complete details on the use and execution of this protocol, please refer to Gopal et al. (2022).1.
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94
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Li SA, Li HG, Shoji N, Desplan C, Chen YCD. Protocol for replacing coding intronic MiMIC and CRIMIC lines with T2A-split-GAL4 lines in Drosophila using genetic crosses. STAR Protoc 2023; 4:102706. [PMID: 38060386 PMCID: PMC10751567 DOI: 10.1016/j.xpro.2023.102706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/30/2023] Open
Abstract
Here, we present a protocol for generating gene-specific split-GAL4 drivers from coding intronic Minos-mediated integration cassette/CRISPR-mediated integration cassette (MiMIC/CRIMIC) lines in Drosophila. We describe steps for four rounds of in vivo genetic crosses, PCR genotyping, and fluorescence imaging to ensure correct orientation of split-GAL4 integration before establishing stable fly stocks. This protocol offers a cost-effective alternative to traditional microinjection techniques for converting coding intronic MiMIC/CRIMIC lines into gene-specific split-GAL4 lines that are adaptable for fly researchers working on different tissues. For complete details on the use and execution of this protocol, please refer to Chen et al.1.
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95
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Levenson MT, Barrere-Cain R, Truong L, Chen YW, Shuck K, Panter B, Reich E, Yang X, Allard P. Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses. STAR Protoc 2023; 4:102756. [PMID: 38043054 PMCID: PMC10730361 DOI: 10.1016/j.xpro.2023.102756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023] Open
Abstract
Caenorhabditis elegans is a valuable model to study organ, tissue, and cell-type responses to external cues. However, the nematode comprises multiple syncytial tissues with spatial coordinates corresponding to distinct nuclear transcriptomes. Here, we present a single-nucleus RNA sequencing (snRNA-seq) protocol that aims to overcome difficulties encountered with single-cell RNA sequencing in C. elegans. We describe steps for isolating C. elegans nuclei for downstream applications including snRNA-seq applied to the context of alcohol exposure. For complete details on the use and execution of this protocol, please refer to Truong et al. (2023).1.
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96
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Li YT, Wu HL, Wu LL. Isolation of murine hepatic myeloid cells with high yield and purity using immunomagnetic beads for subset analysis. STAR Protoc 2023; 4:102592. [PMID: 37742173 PMCID: PMC10520942 DOI: 10.1016/j.xpro.2023.102592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/26/2023] Open
Abstract
There are numerous established techniques for isolating hepatic myeloid cells; however, preserving their phenotypic and functional characteristics can be challenging. We present a straightforward and efficient method to isolate hepatic myeloid cells, including Kupffer cells and lymphocyte antigen 6 complex, locus C+ (Ly6C+) monocytes/macrophages. The procedure involves perfusion of the liver with collagenase and purification with immunomagnetic particles. This protocol ensures the isolation of large quantities of purified, viable, and functional cells without influencing their physiological characteristics. For complete details on the use and execution of this protocol, please refer to Wu et al. (2019).1.
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97
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Antson H, Huang Y, Tõnissoo T, Shimmi O. Conditional knockdown protocol for studying cellular communication using Drosophila melanogaster wing imaginal disc. STAR Protoc 2023; 4:102566. [PMID: 37768826 PMCID: PMC10550844 DOI: 10.1016/j.xpro.2023.102566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023] Open
Abstract
Apicobasal polarity determinants are potential tumor suppressors that have been extensively studied. However, the precise mechanisms by which their misregulation disrupts tissue homeostasis are not fully understood. Here, we present a comprehensive protocol for establishing a conditional RNAi knockdown of scribble in Drosophila wing imaginal disc. We describe steps for generating fly lines, conditional knockdown in host stocks, and sample preparation. We then detail procedures for imaging, image analysis, and verification of wing disc phenotypes by various antibodies. For complete details on the use and execution of this protocol, please refer to Huang et al.1.
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98
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Stephens DC, Mungai M, Crabtree A, Beasley HK, Garza-Lopez E, Vang L, Neikirk K, Vue Z, Vue N, Marshall AG, Turner K, Shao JQ, Sarker B, Murray S, Gaddy JA, Davis J, Damo SM, Hinton AO. Protocol for isolating mice skeletal muscle myoblasts and myotubes via differential antibody validation. STAR Protoc 2023; 4:102591. [PMID: 37938976 PMCID: PMC10663959 DOI: 10.1016/j.xpro.2023.102591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/06/2023] [Accepted: 09/01/2023] [Indexed: 11/10/2023] Open
Abstract
Isolation of skeletal muscles allows for the exploration of many complex diseases. Here, we present a protocol for isolating mice skeletal muscle myoblasts and myotubes that have been differentiated through antibody validation. We describe steps for collecting and preparing murine skeletal tissue, myoblast cell maintenance, plating, and cell differentiation. We then detail procedures for cell incubation, immunostaining, slide preparation and storage, and imaging for immunofluorescence validation.
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99
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Herrera-Ubaldo H, Nájera-González HR, Luna-García V, Marsch-Martínez N, de Folter S. Hormone immunolabeling in resin-embedded Arabidopsis tissues. STAR Protoc 2023; 4:102514. [PMID: 37573503 PMCID: PMC10448208 DOI: 10.1016/j.xpro.2023.102514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
Here, we present a protocol for immunolabeling of molecules in Arabidopsis tissues. We describe steps for tissue fixation and embedding in resin of microtome-derived sections, immunolabeling using fluorescent and non-fluorescent secondary antibodies, and visualization of cytokinin and auxin molecules. This protocol is suitable to study reproductive structures such as inflorescences, flowers, fruits, and tissue-culture-derived samples. This protocol is useful for studying the distribution of a wide range of molecules including hormones and cell wall components. For complete details on the use and execution of this protocol, please refer to Herrera-Ubaldo et al. (2019).1.
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Tse SY, Pukkila-Worley R. Protocol to assess receptor-ligand binding in C. elegans using adapted thermal shift assays. STAR Protoc 2023; 4:102477. [PMID: 37527042 PMCID: PMC10415787 DOI: 10.1016/j.xpro.2023.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/15/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
The Caenorhabditis elegans genome encodes a greatly expanded number of nuclear hormone receptors, many of which remain orphaned. Here, we present a protocol to assess ligand-receptor binding in C. elegans using an adapted cellular thermal shift assay and isothermal dose response. We describe steps for growing C. elegans and preparing lysates and compounds. We also detail how to perform and quantify these assays. This protocol can be used to study any soluble receptor. For complete details on the use and execution of this protocol, please refer to Peterson et al. (2023).1.
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