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Protocol for assessing BMP9-induced angiogenic and osteogenic activity in vitro and in vivo. 体外和体内评估bmp9诱导的血管生成和成骨活性的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-13 DOI: 10.1016/j.xpro.2026.104894
Jianing Duan, Yuanyuan Zhang, Weida Zhang, Xiaohong Qin, Li-Zhi Mi
{"title":"Protocol for assessing BMP9-induced angiogenic and osteogenic activity in vitro and in vivo.","authors":"Jianing Duan, Yuanyuan Zhang, Weida Zhang, Xiaohong Qin, Li-Zhi Mi","doi":"10.1016/j.xpro.2026.104894","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104894","url":null,"abstract":"<p><p>BMP9 is an important regulator in angiogenesis, tissue development, and immune response. Here, we present a protocol to examine the regulatory mechanism of unprocessed BMP9 precursor in BMP9 signaling. We describe procedures for assessing BMP9-induced angiogenic and osteogenic activity in vitro and in vivo. We describe steps for their assessment using flow cytometric analysis, C2C12 differentiation assay, chicken embryo chorioallantoic membrane assay, and mouse subcutaneous Matrigel assay. For complete details on the use and execution of this protocol, please refer to Zhang et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104894"},"PeriodicalIF":1.4,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149184753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo. 制备人体器官型肺培养物以研究呼吸道病毒感染和评估体外抗病毒药物的无琼脂糖方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-13 DOI: 10.1016/j.xpro.2026.104896
Lola Canus, Florentine Jacolin, Virginie Vasseur, Adeline Cezard, Eva Ogire, Anne Aublin-Gex, Amelie Bourgeais, Camille David, Alexandra Erny, Fabienne Archer, Antoine Legras, Damien Sizaret, Antoine Guillon, Vincent Lotteau, Pierre-Olivier Vidalain, Mustapha Si-Tahar, Laure Perrin-Cocon, Cyrille Mathieu
{"title":"Agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo.","authors":"Lola Canus, Florentine Jacolin, Virginie Vasseur, Adeline Cezard, Eva Ogire, Anne Aublin-Gex, Amelie Bourgeais, Camille David, Alexandra Erny, Fabienne Archer, Antoine Legras, Damien Sizaret, Antoine Guillon, Vincent Lotteau, Pierre-Olivier Vidalain, Mustapha Si-Tahar, Laure Perrin-Cocon, Cyrille Mathieu","doi":"10.1016/j.xpro.2026.104896","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104896","url":null,"abstract":"<p><p>Here, we present a protocol to generate human organotypic lung cultures from surgical lung resection for the study of respiratory infections. We describe steps for tissue harvesting, biopsy punching, mechanical slicing, and culture at the air-liquid interface. This technique enables robust ex vivo infections of human lung tissues with respiratory viruses, including influenza A and Nipah. It can be used to study host-pathogen interactions, analyze innate immune responses, and evaluate antiviral candidates in physiologically relevant human lung tissue. For complete details on the use and execution of this protocol, please refer to Cezard et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104896"},"PeriodicalIF":1.4,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149184771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for an immunocompetent KPC mouse model of pancreatic cancer resection and recurrence for perioperative treatment studies. 胰腺癌切除术及围手术期复发免疫活性KPC小鼠模型的研究方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-10 DOI: 10.1016/j.xpro.2026.104897
Jacob L Léger, Nawal Amhis, Sarah Mansouri, Maria Fernanda Meza Pacheco, Lauren Daniel, Hugo Giguère, Yves Collin, Lee-Hwa Tai
{"title":"Protocol for an immunocompetent KPC mouse model of pancreatic cancer resection and recurrence for perioperative treatment studies.","authors":"Jacob L Léger, Nawal Amhis, Sarah Mansouri, Maria Fernanda Meza Pacheco, Lauren Daniel, Hugo Giguère, Yves Collin, Lee-Hwa Tai","doi":"10.1016/j.xpro.2026.104897","DOIUrl":"10.1016/j.xpro.2026.104897","url":null,"abstract":"<p><p>In mouse models of pancreatic ductal adenocarcinoma, surgical removal of orthotopic tumors typically involves removing the primary tumor along with the spleen. Here, we present a protocol for surgical removal of the tumor in the tail of the pancreas while preserving the spleen. We describe steps for implantation of mouse pancreatic cancer cells followed by the identification and removal of the orthotopic tumor. We also outline perioperative treatment strategies for tumor recurrence.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104897"},"PeriodicalIF":1.4,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for endothelial cell-derived extracellular vesicle isolation and characterization. 内皮细胞来源的细胞外囊泡分离和表征方法。
IF 1.4
STAR Protocols Pub Date : 2026-10-09 DOI: 10.1016/j.xpro.2026.104887
Charlotte Hooper, Naveed Akbar
{"title":"Protocol for endothelial cell-derived extracellular vesicle isolation and characterization.","authors":"Charlotte Hooper, Naveed Akbar","doi":"10.1016/j.xpro.2026.104887","DOIUrl":"10.1016/j.xpro.2026.104887","url":null,"abstract":"<p><p>Endothelial cells regulate intercellular and inter-organ communication through extracellular vesicles (EVs), which have diagnostic and therapeutic potential. We describe single-particle interferometric reflectance imaging directly from culture supernatants, followed by ultracentrifugation isolation of EVs. We determine EV size and concentration by nanoparticle tracking analysis and characterize EVs by western blotting and transmission electron microscopy. This protocol can be applied to other cell systems of EV biology. For details on the execution of this protocol, please refer to Timms et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104887"},"PeriodicalIF":1.4,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections and constructing sequencing libraries. 从胰腺癌FFPE切片中分离高质量细胞核和构建测序文库的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104880
Huiheng Ning, Wei Zhou, Kang Chen, Qinhang Gao, Jieying Pan, Min-Min Chen
{"title":"Protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections and constructing sequencing libraries.","authors":"Huiheng Ning, Wei Zhou, Kang Chen, Qinhang Gao, Jieying Pan, Min-Min Chen","doi":"10.1016/j.xpro.2026.104880","DOIUrl":"10.1016/j.xpro.2026.104880","url":null,"abstract":"<p><p>Formalin-fixed paraffin-embedded (FFPE) tissues are archived resources for biomedical research but challenging for single-cell transcriptomic analysis. Here, we present a protocol for isolating high-quality nuclei from FFPE pancreatic cancer sections. We describe steps for deparaffinization, enzymatic digestion, nuclei purification, and library construction using the 10× Genomics Fixed RNA Profiling platform. This protocol enables transcriptomic profiling of archived clinical specimens at single-nucleus resolution. For complete details on the use and execution of this protocol, please refer to Chen et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104880"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13676707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA. 使用ThermOptCOBRA进行代谢网络的热力学优化构建和分析的协议。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104890
Pavan Kumar, Nirav Pravinbhai Bhatt
{"title":"Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.","authors":"Pavan Kumar, Nirav Pravinbhai Bhatt","doi":"10.1016/j.xpro.2026.104890","DOIUrl":"10.1016/j.xpro.2026.104890","url":null,"abstract":"<p><p>Thermodynamically infeasible cycles violate the second law of thermodynamics but are permitted by stoichiometric flux analysis. Here, we present a protocol for the construction and analysis of metabolic networks using ThermOptCOBRA, a MATLAB extension of the COBRA Toolbox. We describe steps for enumerating cycles (ThermOptEnumerator), determining feasible directions and blocked reactions (ThermOptCC), and building thermodynamically consistent context-specific models using omics data (ThermOptiCS). We then detail procedures for removing loops or sample loopless flux distributions (ThermOptFlux/ADSB-ThermOptFlux). For complete details on the use and execution of this protocol, please refer to Kumar and Bhatt.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104890"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration. 使用scRNA-seq和CUT&RUN集成确定小鼠肢体软骨形成过程中Sox9靶程序的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104889
Kohei Kita, Masayasu Sega, Yutaro Uchida, Tomoki Chiba, Takahide Matsushima, Hiroshi Asahara
{"title":"Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.","authors":"Kohei Kita, Masayasu Sega, Yutaro Uchida, Tomoki Chiba, Takahide Matsushima, Hiroshi Asahara","doi":"10.1016/j.xpro.2026.104889","DOIUrl":"10.1016/j.xpro.2026.104889","url":null,"abstract":"<p><p>Developing tissues comprise heterogeneous cell populations exhibiting stage-dependent transcriptional dynamics. We present a protocol to identify candidate Sox9 target genes in specific murine cell populations by integrating single-cell RNA sequencing (scRNA-seq) with Ty1-tag-based CUT&RUN. We describe steps for embryonic forelimb bud dissection, scRNA-seq and CUT&RUN sample and library preparation, and data processing. We then detail procedures for integrative analysis of stage- and cluster-specific Sox9 targets. The framework may be adaptable to other Sox9-expressing tissues and developmental stages with appropriate optimization. For complete details on the use and execution of this protocol, please refer to Sega et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104889"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149148186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease. 在阿尔茨海默病小鼠模型的皮层中使用长读DNA测序进行全基因组差异甲基化的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104827
Ümran Yaman, Emil Gustavsson, Jasmaine Lee, Hermione Ugolini, Hannah Macpherson, Paige Mumford, Frances Wiseman, John Hardy, Dervis A Salih
{"title":"Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.","authors":"Ümran Yaman, Emil Gustavsson, Jasmaine Lee, Hermione Ugolini, Hannah Macpherson, Paige Mumford, Frances Wiseman, John Hardy, Dervis A Salih","doi":"10.1016/j.xpro.2026.104827","DOIUrl":"10.1016/j.xpro.2026.104827","url":null,"abstract":"<p><p>Third-generation sequencing enables direct detection of genome-wide 5-methylcytosine without bisulfite conversion. Here, we present a protocol for generating long-read DNA sequencing from mouse cortex and performing genome-wide differential methylation analysis. We describe steps for high-molecular-weight DNA extraction, data generation, and downstream analysis. We demonstrate the workflow in the App<sup>NL-G-F</sup> mouse model of amyloid pathology and provide a reproducible pipeline that links modified-base BAM (modBAM) files to annotated differentially methylated regions and functional enrichment results.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104827"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149149222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for scalable production of orally deliverable R-spondin1-loaded small extracellular vesicles for WNT-signaling activation and tissue regeneration. 用于wnt信号激活和组织再生的可口服r -spondin1负载小细胞外囊泡的规模化生产方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104891
Lingyan Yang, Ting Jiang, Shixiang Wang, Yue Yang, Zhiping Qiao, Yun-Shen Chan
{"title":"Protocol for scalable production of orally deliverable R-spondin1-loaded small extracellular vesicles for WNT-signaling activation and tissue regeneration.","authors":"Lingyan Yang, Ting Jiang, Shixiang Wang, Yue Yang, Zhiping Qiao, Yun-Shen Chan","doi":"10.1016/j.xpro.2026.104891","DOIUrl":"10.1016/j.xpro.2026.104891","url":null,"abstract":"<p><p>R-spondin1 plays a pivotal role in potentiating canonical WNT/β-catenin signaling, a pathway critical for maintaining stem cell homeostasis and driving tissue regeneration. Here, we present a scalable, serum-free protocol for producing R-spondin1-loaded small extracellular vesicles (evRSPO1) from engineered HEK293 cells, with multimodal characterization of vesicle quality and bioactivity. We also describe steps for in vitro functional validation of the vesicles using mouse intestinal organoids and for in vivo therapeutic applications in mouse intestinal regeneration via oral delivery. For complete details on the use and execution of this protocol, please refer to Yang et al.<sup>1</sup><sup>,</sup><sup>2</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104891"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13676708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for establishing a murine Toscana virus infection model and downstream cellular analysis of skin tissue and cells. 建立小鼠托斯卡纳病毒感染模型及皮肤组织和细胞下游细胞分析方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-08 DOI: 10.1016/j.xpro.2026.104885
Yonca Keskek Turk, Ailish McCafferty-Brown, Clive S McKimmie
{"title":"Protocol for establishing a murine Toscana virus infection model and downstream cellular analysis of skin tissue and cells.","authors":"Yonca Keskek Turk, Ailish McCafferty-Brown, Clive S McKimmie","doi":"10.1016/j.xpro.2026.104885","DOIUrl":"10.1016/j.xpro.2026.104885","url":null,"abstract":"<p><p>Here, we present an in vivo approach to study virus-vector-host interactions during Toscana virus (TOSV) infection in mouse skin. We describe preparation of viral stocks and subcutaneous TOSV inoculation into dorsal upper foot skin, either alone, with sand-fly salivary gland extract (SGE), or following sand-fly biting. We then detail tissue collection and generation of single-cell suspensions. Finally, we describe flow cytometric detection of infected cells, magnetic isolation of dermal fibroblasts, and RNA extraction for transcriptomic analysis. For complete details on the use and execution of this protocol, please refer to Keskek Turk et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104885"},"PeriodicalIF":1.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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