发布求助
文献互助 智能选刊 最新文献

STAR Protocols最新文献

筛选
英文 中文
Protocol for characterizing craniopharyngioma subtypes and their microenvironments using single-cell RNA sequencing and immunohistochemistry. 使用单细胞RNA测序和免疫组织化学表征颅咽管瘤亚型及其微环境的方案。
IF 1.3
STAR Protocols Pub Date : 2025-04-14 DOI: 10.1016/j.xpro.2025.103760
Takashi Kono, Tatsuma Matsuda, Masanori Fujimoto, Yuki Taki, Ikki Sakuma, Naoko Hashimoto, Yasuhiro Nakamura, Kentaro Horiguchi, Yoshinori Higuchi, Atsushi Onodera, Takashi Miki, Tomoaki Tanaka
{"title":"Protocol for characterizing craniopharyngioma subtypes and their microenvironments using single-cell RNA sequencing and immunohistochemistry.","authors":"Takashi Kono, Tatsuma Matsuda, Masanori Fujimoto, Yuki Taki, Ikki Sakuma, Naoko Hashimoto, Yasuhiro Nakamura, Kentaro Horiguchi, Yoshinori Higuchi, Atsushi Onodera, Takashi Miki, Tomoaki Tanaka","doi":"10.1016/j.xpro.2025.103760","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103760","url":null,"abstract":"<p><p>Here, we present a comprehensive protocol for analyzing craniopharyngioma subtypes and their tumor microenvironments at single-cell resolution. We describe tumor tissue dissociation, single-cell isolation, RNA sequencing library preparation, and bioinformatics analysis procedures. We also detail immunohistochemistry procedures for validating findings. This approach enables the detailed characterization of tumor cellular composition, immune cell networks, and molecular signatures that distinguish adamantinomatous from papillary craniopharyngiomas. For complete details on the use and execution of this protocol, refer to Matsuda et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103760"},"PeriodicalIF":1.3,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12022695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144043969","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 implementing the nested model for AI design and validation in compliance with AI regulations. 用于实现AI设计和验证的嵌套模型的协议，以符合AI规则。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103771
Akshat Dubey, Zewen Yang, Aleksandar Anžel, Georges Hattab
{"title":"Protocol for implementing the nested model for AI design and validation in compliance with AI regulations.","authors":"Akshat Dubey, Zewen Yang, Aleksandar Anžel, Georges Hattab","doi":"10.1016/j.xpro.2025.103771","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103771","url":null,"abstract":"<p><p>Here, we present a protocol for implementing the nested model for developing and validating artificial intelligence (AI) systems in compliance with AI regulations. We describe steps for defining the regulations and associated ethical and technical key requirements through the potential research questions. We then detail the procedures for designing and validating an AI application across the domain, data, model, and prediction layers, enabling users to interact with layers through a front-end interface. For complete information on the generation and use of this protocol, please refer to Dubey et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103771"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019447","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 nuclei from frozen fish heart tissue for single-cell genomic assays. 从冷冻鱼心脏组织中分离细胞核用于单细胞基因组分析的规程。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103765
Chaoguang Wei, Ruonan Jia, Adelino V M Canário, Liangbiao Chen, Qianghua Xu, Peng Hu
{"title":"Protocol for isolating nuclei from frozen fish heart tissue for single-cell genomic assays.","authors":"Chaoguang Wei, Ruonan Jia, Adelino V M Canário, Liangbiao Chen, Qianghua Xu, Peng Hu","doi":"10.1016/j.xpro.2025.103765","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103765","url":null,"abstract":"<p><p>Unbiased isolation of intact single nuclei from complex tissues, such as cryopreserved hearts, for massively parallel single-cell genomic assays is particularly challenging. Here, we present a protocol for isolating high-quality nuclei from the heart tissue of Trematomus bernacchii, an Antarctic fish species with notoriously challenging tissue for nuclear extraction. We describe steps for pulverizing frozen heart tissue, library construction, and sequencing. This protocol can provide a valuable reference for isolating nuclei from other cryopreserved marine fish tissues.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103765"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037316","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 study the genomic profile of histone lactylation with CUT&RUN assay in tumor-associated macrophages. 在肿瘤相关巨噬细胞中使用CUT&RUN试验研究组蛋白乳酸化的基因组图谱。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103766
Alessandra De Leo, Alessio Ugolini, Filippo Veglia
{"title":"Protocol to study the genomic profile of histone lactylation with CUT&RUN assay in tumor-associated macrophages.","authors":"Alessandra De Leo, Alessio Ugolini, Filippo Veglia","doi":"10.1016/j.xpro.2025.103766","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103766","url":null,"abstract":"<p><p>Lysine lactylation is a distinctive histone modification that plays a crucial role in epigenetic regulation and gene transcription. Here, we present a protocol for studying the genomic profile of histone lactylation with the CUT&RUN assay in tumor-associated macrophages. We describe steps for preparing live cells, gating strategies for isolating glucose transporter type 1 + (GLUT1+) monocyte-derived macrophages (MDMs) by fluorescence-activated cell sorting (FACS), binding lactyl-specific primary antibodies, and quantifying DNA using qPCR. This protocol is applicable to both tumor-derived and in-vitro-generated bone-marrow-derived macrophages. For complete details on the use and execution of this protocol, please refer to De Leo et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103766"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040112","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 the purification, analysis, and handling of acyl carrier proteins from type I fatty acid and polyketide synthases. 从I型脂肪酸和聚酮合酶中纯化、分析和处理酰基载体蛋白的程序。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103762
Christian Gusenda, Svenja Berlage, Ines Burkhart, Benjamin Chagot, Kira J Weissman, Harald Schwalbe, Martin Grininger
{"title":"Protocol for the purification, analysis, and handling of acyl carrier proteins from type I fatty acid and polyketide synthases.","authors":"Christian Gusenda, Svenja Berlage, Ines Burkhart, Benjamin Chagot, Kira J Weissman, Harald Schwalbe, Martin Grininger","doi":"10.1016/j.xpro.2025.103762","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103762","url":null,"abstract":"<p><p>Acyl carrier proteins (ACPs) are key domains in fatty acid and polyketide synthases (PKSs), shuttling intermediates to catalytic partners. Here, we present a protocol for purifying and analyzing ACPs from fatty acid synthases (FASs) and PKSs, using four model ACPs from Mus musculus, Saccharopolyspora erythraea, Streptomyces venezuelae, and Streptomyces hygroscopicus. We describe steps for recombinant ACP production in E. coli; purification via chromatography or precipitation; ACP modification (holo/acyl forms); and analysis using urea PAGE, high-performance liquid chromatography (HPLC), and NMR spectroscopy. For complete details on the use and execution of this protocol, please refer to Gusenda et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103762"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989418","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 measuring membrane elasticity of mouse cardiomyocytes using atomic force microscopy. 用原子力显微镜测量小鼠心肌细胞膜弹性的方法。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103746
Andrés David Morales Maldonado, Daphne Agostina Diloretto, Valeriy Timofeyev, Arpad Karsai, Evgeny Ogorodnik, Yuqi Huang, Ning Zong, Gang-Yu Liu, Nipavan Chiamvimonvat, Xiao-Dong Zhang
{"title":"Protocol for measuring membrane elasticity of mouse cardiomyocytes using atomic force microscopy.","authors":"Andrés David Morales Maldonado, Daphne Agostina Diloretto, Valeriy Timofeyev, Arpad Karsai, Evgeny Ogorodnik, Yuqi Huang, Ning Zong, Gang-Yu Liu, Nipavan Chiamvimonvat, Xiao-Dong Zhang","doi":"10.1016/j.xpro.2025.103746","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103746","url":null,"abstract":"<p><p>Atomic force microscopy (AFM) is a powerful technique that enables the determination of cellular mechanics at the single-cell level. Here, we present a protocol for using AFM to measure membrane mechanical properties of mouse ventricular cardiomyocytes. The key steps include isolation of mouse cardiomyocytes, cantilever preparation, modification and calibration, and measurement of force-deformation profiles, from which membrane Young's moduli are quantified. The outcomes advance our knowledge of cardiomyocyte's unique mechanical and dynamic properties.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103746"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019449","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 extraction and characterization of mouse brain-derived extracellular matrix for neuronal cell culture. 用于神经细胞培养的小鼠脑源性细胞外基质的提取和表征方法。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103764
Weihao Zhao, Ziqian Liu, Zhenghao Li, Hao Qian, Jing Hu
{"title":"Protocol for extraction and characterization of mouse brain-derived extracellular matrix for neuronal cell culture.","authors":"Weihao Zhao, Ziqian Liu, Zhenghao Li, Hao Qian, Jing Hu","doi":"10.1016/j.xpro.2025.103764","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103764","url":null,"abstract":"<p><p>Neuronal cell cultures are highly sensitive to their microenvironment, particularly the choice of coating substrate. Here, we present a protocol to isolate extracellular matrix (ECM) from mouse brain tissue, providing a native coating material that closely mimics in vivo conditions. We detail decellularization steps, guidelines for measuring ECM quality, and instructions for co-culturing neuronal cells on the resulting substrate. By promoting improved neuronal survival, growth, and differentiation, this protocol has broad implications for in vitro neurobiological research and downstream applications.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103764"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985910","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 identify proteins as regulators of gene expression noise. 鉴定蛋白作为基因表达噪声调节因子的方案。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103763
Óscar García-Blay, Maike M K Hansen
{"title":"Protocol to identify proteins as regulators of gene expression noise.","authors":"Óscar García-Blay, Maike M K Hansen","doi":"10.1016/j.xpro.2025.103763","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103763","url":null,"abstract":"<p><p>Noise regulatory proteins are key to understanding the dynamic regulation of cell-to-cell heterogeneity in gene expression. Here, we present a protocol for identifying novel candidate proteins with noise regulatory functions. We describe steps for inhibiting translation in cells, performing single-cell RNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS), and utilizing known regulator-target interactions to integrate obtained data in a regulator enrichment analysis. This protocol has the potential to be applied in any cell line and under culture conditions of choice. For complete details on the use and execution of this protocol, please refer to García-Blay et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103763"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144015218","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 the analysis of cell-free DNA end characteristics for accurate cancer diagnosis. 分析细胞游离DNA末端特征以准确诊断癌症的方案。
IF 1.3
STAR Protocols Pub Date : 2025-04-11 DOI: 10.1016/j.xpro.2025.103757
Xiaoyi Liu, Fanglei Gong, Huizhen Lin, Yunyun An, Kun Sun
{"title":"Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis.","authors":"Xiaoyi Liu, Fanglei Gong, Huizhen Lin, Yunyun An, Kun Sun","doi":"10.1016/j.xpro.2025.103757","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103757","url":null,"abstract":"<p><p>Fragmentation patterns of plasma cell-free DNA (cfDNA) are promising biomarkers in cancer diagnosis. Here, we present a protocol to enrich tumor-derived cfDNA molecules through end selection. We describe steps for installing software, aligning plasma cfDNA data to the reference genome, and performing end selection on cfDNA. We then detail procedures for building cancer diagnostic models with artificial intelligence. Overall, we provide commands to align cfDNA whole-genome sequencing data starting from raw reads, then extract fragmentomic features, and finally build diagnostic models with performance evaluations. For complete information on the generation and use of this protocol, please refer to Ju et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103757"},"PeriodicalIF":1.3,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999372","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 assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder. 协议组装，优先排序，并表征piRNA集群使用piRNA集群构建器。
IF 1.3
STAR Protocols Pub Date : 2025-04-10 DOI: 10.1016/j.xpro.2025.103759
Franziska Ahrend, Parthena Konstantinidou, Zuzana Loubalova, Yuejun Wang, Hernan Lorenzi, Gunter Meister, Astrid D Haase
{"title":"Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder.","authors":"Franziska Ahrend, Parthena Konstantinidou, Zuzana Loubalova, Yuejun Wang, Hernan Lorenzi, Gunter Meister, Astrid D Haase","doi":"10.1016/j.xpro.2025.103759","DOIUrl":"https://doi.org/10.1016/j.xpro.2025.103759","url":null,"abstract":"<p><p>PIWI-interacting RNAs (piRNAs) play a critical role in safeguarding genome integrity in germ cells, ensuring fertility. Here, we provide a protocol for processing piRNA sequencing data, identifying piRNA-rich genomic regions as piRNA clusters, and preparing these clusters for downstream analyses. We describe steps for assembling piRNA cluster regions using an R-based tool, the piRNA Cluster Builder (PICB), which integrates unique and multimapping piRNA reads stepwise. The protocol allows for parameter optimizations and generates normalized outputs for prioritization of piRNA clusters. For complete details on the use and execution of this protocol, please refer to Konstantinidou et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 2","pages":"103759"},"PeriodicalIF":1.3,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030658","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
首页 上一页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信