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Protocol for Cas9 nickase-mediated induction and two-dimensional gel detection of i-loops at human telomeric and alpha satellite repeats. Cas9镍酶介导的人类端粒和α卫星重复序列i环诱导和二维凝胶检测方案
IF 1.4
STAR Protocols Pub Date : 2026-10-06 DOI: 10.1016/j.xpro.2026.104888
Elia Zanella, Flavia Bruno, Ylli Doksani
{"title":"Protocol for Cas9 nickase-mediated induction and two-dimensional gel detection of i-loops at human telomeric and alpha satellite repeats.","authors":"Elia Zanella, Flavia Bruno, Ylli Doksani","doi":"10.1016/j.xpro.2026.104888","DOIUrl":"10.1016/j.xpro.2026.104888","url":null,"abstract":"<p><p>Single-stranded DNA breaks (SSBs) at repetitive elements promote internal loops (i-loops), precursors of extrachromosomal circular DNA (eccDNA). Here, we present a protocol for inducing targeted breaks at human telomeric or alpha-satellite repeats using doxycycline-inducible Cas9 nickase variants and repeat-specific sgRNAs. We describe steps for verifying strand-specific nicking by alkaline-gel Southern blotting and detecting i-loop accumulation by two-dimensional agarose gel electrophoresis (2D gel). In this protocol, DNase I treatment of isolated nuclei is employed as a Cas9-independent control. For complete details on the use and execution of this protocol, please refer to Zanella et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104888"},"PeriodicalIF":1.4,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115791","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 analyzing tumor-infiltrating bystander CD8+ T cells in mice using adoptive transfer of P14 TCR-transgenic CD8+ T cells. 使用P14 tcr转基因CD8+ T细胞过继转移分析小鼠肿瘤浸润的旁观者CD8+ T细胞的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-06 DOI: 10.1016/j.xpro.2026.104886
Chunyang Xie, Wenwen Xi, Hairu Wang, Lilin Ye, Xiangyu Chen, Yao Lin
{"title":"Protocol for analyzing tumor-infiltrating bystander CD8<sup>+</sup> T cells in mice using adoptive transfer of P14 TCR-transgenic CD8<sup>+</sup> T cells.","authors":"Chunyang Xie, Wenwen Xi, Hairu Wang, Lilin Ye, Xiangyu Chen, Yao Lin","doi":"10.1016/j.xpro.2026.104886","DOIUrl":"10.1016/j.xpro.2026.104886","url":null,"abstract":"<p><p>While tumor-specific CD8<sup>+</sup> T cells become functionally exhausted within the tumor microenvironment (TME), virus-specific bystander memory CD8<sup>+</sup> T (T<sub>BYS</sub>) cells are abundant and represent valuable immunotherapy targets. Here, we present a protocol to analyze tumor-infiltrating virus-specific T<sub>BYS</sub> cells in murine tumor models using P14 CD8<sup>+</sup> T cells. We describe steps for monitoring long-term in vivo behavior of P14 T<sub>BYS</sub> cells and characterizing their differentiation trajectories and functional heterogeneity. For complete details on the use and execution of this protocol, please refer to Lin et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104886"},"PeriodicalIF":1.4,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115789","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 chronic electroencephalography, fiber photometry, and silicon probe recordings in the Syrian hamster. 叙利亚仓鼠慢性脑电图、纤维光度测定和硅探针记录的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-05 DOI: 10.1016/j.xpro.2026.104863
Fuki Yamashita, Ren Y Sato, Yasutaka Mukai, Hiroaki Nishimura, Sarah Dagher, Shimpei Ishiyama, Miyu Kimata, Riho Kobayashi, Hiroaki Norimoto
{"title":"Protocol for chronic electroencephalography, fiber photometry, and silicon probe recordings in the Syrian hamster.","authors":"Fuki Yamashita, Ren Y Sato, Yasutaka Mukai, Hiroaki Nishimura, Sarah Dagher, Shimpei Ishiyama, Miyu Kimata, Riho Kobayashi, Hiroaki Norimoto","doi":"10.1016/j.xpro.2026.104863","DOIUrl":"10.1016/j.xpro.2026.104863","url":null,"abstract":"<p><p>The Syrian hamster (Mesocricetus auratus) exhibits a unique metabolic physiology, including the ability to enter hypometabolic states. While this species represents a powerful model for studying the neuronal basis of metabolic control and brain-state transitions, its use is limited due to the lack of detailed protocols for chronic neuronal measurements. Here, we present a step-by-step protocol for chronic surgical implantation and multimodal neuronal recordings in Syrian hamsters. We describe steps for electroencephalography (EEG), fiber photometry, and multi-channel silicon probe recordings.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104863"},"PeriodicalIF":1.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115769","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 standardized minimally invasive mouse models of bisphosphonate-related and radiation-induced jaw osteonecrosis. 标准化微创双膦酸盐相关和辐射诱发的颌骨骨坏死小鼠模型的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-05 DOI: 10.1016/j.xpro.2026.104851
Zhangfan Ding, Jiayuan Zhang, Hanyu Liu, Abhishek Chandra, Makarand V Risbud, Anjali P Kusumbe, Junyu Chen
{"title":"Protocol for standardized minimally invasive mouse models of bisphosphonate-related and radiation-induced jaw osteonecrosis.","authors":"Zhangfan Ding, Jiayuan Zhang, Hanyu Liu, Abhishek Chandra, Makarand V Risbud, Anjali P Kusumbe, Junyu Chen","doi":"10.1016/j.xpro.2026.104851","DOIUrl":"10.1016/j.xpro.2026.104851","url":null,"abstract":"<p><p>We present a protocol for establishing murine models of bisphosphonate-related osteonecrosis of the jaw (BRONJ) and osteoradionecrosis of the jaw (ORNJ). We describe steps for a uniform, low-trauma tooth extraction technique with disease-specific induction, systemic zoledronic acid for BRONJ and precision-targeted irradiation for ORNJ, to generate robust and clinically relevant models of jaw osteonecrosis, approaching minimizes procedural variability and off-target effects, yielding robust, clinically relevant phenotypes. This protocol provides a standard and minimally invasive framework for investigating jaw osteonecrosis arising from distinct etiologies.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104851"},"PeriodicalIF":1.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13670947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115810","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 confocal microscopy-based localization of chorismate mutase protein of Mycobacterium tuberculosis in trans-Golgi compartment. 基于共聚焦显微镜的结核分枝杆菌反式高尔基腔中choris酸突变酶蛋白定位方法。
IF 1.4
STAR Protocols Pub Date : 2026-10-05 DOI: 10.1016/j.xpro.2026.104859
Vandana Maurya, Sangita Mukhopadhyay
{"title":"Protocol for confocal microscopy-based localization of chorismate mutase protein of Mycobacterium tuberculosis in trans-Golgi compartment.","authors":"Vandana Maurya, Sangita Mukhopadhyay","doi":"10.1016/j.xpro.2026.104859","DOIUrl":"10.1016/j.xpro.2026.104859","url":null,"abstract":"<p><p>Here, we present a confocal microscopy protocol to determine the localization of Mycobacterium tuberculosis chorismate mutase (MtbCM) in trans-Golgi compartment. We co-transfect HEK293 cells with either pEGFP-C1-MtbCM and mCherry-TGOLN2 (trans-Golgi marker) or pEGFP-C1 and mCherry-TGOLN2 as a control, using Lipofectamine 2000. We describe steps for constructing pEGFP-C1-MtbCM and performing co-transfection and image acquisition using confocal microscopy. This protocol provides a representative procedure to determine the subcellular localization of the mycobacterial protein to the trans-Golgi compartment. For complete details on the use and execution of this protocol, please refer to Pal et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104859"},"PeriodicalIF":1.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115782","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 integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease. 综合转录组学/代谢组学分析方案：影响牡蛎- poms疾病因素的案例研究。
IF 1.4
STAR Protocols Pub Date : 2026-10-03 DOI: 10.1016/j.xpro.2026.104875
Leo Duperret, Alejandro Valdivieso, Bruno Petton, Benjamin Morga, Nicole Faury, Julien de Lorgeril, Charlotte Corporeau, Lionel Degremont, Sylvain Henry, Andrei Turtoi, Juliette Pouzadoux, Océane Romatif, Gaelle Courtay, Cristián J Monaco, Eve Toulza, Arnaud Lagorce, Jeremie Vidal-Dupiol, Guillaume Mitta
{"title":"Protocol for integrative transcriptomic/metabolomic analysis: A case study on factors influencing the oyster-POMS disease.","authors":"Leo Duperret, Alejandro Valdivieso, Bruno Petton, Benjamin Morga, Nicole Faury, Julien de Lorgeril, Charlotte Corporeau, Lionel Degremont, Sylvain Henry, Andrei Turtoi, Juliette Pouzadoux, Océane Romatif, Gaelle Courtay, Cristián J Monaco, Eve Toulza, Arnaud Lagorce, Jeremie Vidal-Dupiol, Guillaume Mitta","doi":"10.1016/j.xpro.2026.104875","DOIUrl":"10.1016/j.xpro.2026.104875","url":null,"abstract":"<p><p>Deciphering the molecular mechanisms underlying complex biological interactions requires comprehensive approaches that capture these interactions across multiple regulatory and functional levels. Here, we present a protocol applied to the host-pathogen-environment interactions underlying Pacific oyster mortality syndrome (POMS) in Magallana gigas. We describe steps from individual transcriptomic and metabolomic workflows using WGCNA and FELLA packages, to their integration in a biologically meaningful framework. This protocol aims to move omics integration beyond statistical correlations toward functional enrichment with cross-validation at the system level. For complete details on the use and execution of this protocol, please refer to Duperret et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104875"},"PeriodicalIF":1.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115796","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
Modeling human tumor evolution in mice. 在小鼠中模拟人类肿瘤进化。
IF 1.4
STAR Protocols Pub Date : 2026-10-03 DOI: 10.1016/j.xpro.2026.104872
Dale M Watt, Louise E Mitchell, S Leah Etheridge, Philip D Dunne, Daniel J Murphy, Karen Blyth
{"title":"Modeling human tumor evolution in mice.","authors":"Dale M Watt, Louise E Mitchell, S Leah Etheridge, Philip D Dunne, Daniel J Murphy, Karen Blyth","doi":"10.1016/j.xpro.2026.104872","DOIUrl":"10.1016/j.xpro.2026.104872","url":null,"abstract":"<p><p>Cancer develops through an evolutionary process driven by mutation and selective pressures imposed by the microenvironment. To be translationally relevant, experimental models must recapitulate these clinical complexities. In this Primer, we consider how different mouse-modeling strategies can be aligned with human tumor evolution, focusing on mutation order, the emergence and competition of initially rare mutant clones within genetically mosaic tissues, and microenvironmental context. By comparing conventional genetically engineered mouse models (GEMMs), transplant-based models, and emerging tools such as somatic editing and the tandem arrayed regulator (TAR) allele system, we offer a guide for selecting the most appropriate mouse model to address specific evolutionary questions.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104872"},"PeriodicalIF":1.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115624","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 generating highly enriched sex-specific primary cortical astrocytes from individual mouse pups. 从单个小鼠幼崽中产生高度富集的性别特异性初级皮质星形胶质细胞的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-03 DOI: 10.1016/j.xpro.2026.104873
Sanarya Al-Jaf, En-Hung Ai, Julia A Wilson, Khaled S Abd-Elrahman
{"title":"Protocol for generating highly enriched sex-specific primary cortical astrocytes from individual mouse pups.","authors":"Sanarya Al-Jaf, En-Hung Ai, Julia A Wilson, Khaled S Abd-Elrahman","doi":"10.1016/j.xpro.2026.104873","DOIUrl":"10.1016/j.xpro.2026.104873","url":null,"abstract":"<p><p>Here, we present a protocol for generating highly enriched primary cortical astrocytes from individual neonatal mouse pups. We describe steps for mechanically dissociating cortical tissue, culturing in coated flasks, and removing oligodendrocyte progenitor cells through mechanical shaking and selective pharmacological depletion of microglia. We then detail procedures for PCR-based analysis of tail-biopsy DNA to determine sex and genotype to genetically define astrocyte cultures. This protocol enables the investigation of sex- and genotype-specific mechanisms while avoiding the confounding effects of pooled tissue.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104873"},"PeriodicalIF":1.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115751","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 detecting germline copy number variants from whole-exome sequencing using agent-assisted Snakemake workflows. 使用试剂辅助的Snakemake工作流程从全外显子组测序中检测种系拷贝数变异的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-03 DOI: 10.1016/j.xpro.2026.104883
Xiang Chen
{"title":"Protocol for detecting germline copy number variants from whole-exome sequencing using agent-assisted Snakemake workflows.","authors":"Xiang Chen","doi":"10.1016/j.xpro.2026.104883","DOIUrl":"10.1016/j.xpro.2026.104883","url":null,"abstract":"<p><p>Germline copy number variants (gCNVs) are vital for diagnosing rare monogenic disorders. Here, we present a containerized, agent-assisted Snakemake protocol for detecting, annotating, and visualizing gCNVs from short-read whole-exome sequencing data. We describe steps for constructing baseline models, executing CNV calling, annotating variant pathogenicity using public datasets, and rendering interactive visual reports. This automated workflow simplifies routine management and ensures cross-platform reproducibility through a unified interface.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104883"},"PeriodicalIF":1.4,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13660657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115774","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 rolling circle amplification-based nanopore sequencing of eccDNA from cell and plasma samples. 基于滚动环扩增的细胞和血浆样品中eccDNA纳米孔测序方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-02 DOI: 10.1016/j.xpro.2026.104865
Biyuan Miao, Xinlei Huang, Hui Chen, Wang Li, Qingsong Zen, Huaxi Li, Jia Gu, Pingping Xu, Shaogui Wan
{"title":"Protocol for rolling circle amplification-based nanopore sequencing of eccDNA from cell and plasma samples.","authors":"Biyuan Miao, Xinlei Huang, Hui Chen, Wang Li, Qingsong Zen, Huaxi Li, Jia Gu, Pingping Xu, Shaogui Wan","doi":"10.1016/j.xpro.2026.104865","DOIUrl":"10.1016/j.xpro.2026.104865","url":null,"abstract":"<p><p>Extrachromosomal circular DNAs (eccDNAs) can drive copy number variation and genomic rearrangements and act as mobile regulators of gene expression. Here, we detail a protocol for eccDNA identification from cell and plasma samples. We describe steps for sample preprocessing with circular DNA enrichment, rolling-circle amplification and debranching, library preparation and sequencing, along with quality control tailored to the key steps. For complete details on the use and execution of this protocol, please refer to Li et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104865"},"PeriodicalIF":1.4,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115772","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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