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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
Protocol to evaluate markers of reactive oxygen species and labile iron from a single sample across in vitro and in in vivo lung cancer models. 在体外和体内肺癌模型中评估单个样品中活性氧和不稳定铁的标记物的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-02 DOI: 10.1016/j.xpro.2026.104893
Jennifer A Petsche, Sunny C Huang, Danielle J Foster, Charles C Searby, Val C Sheffield, Douglas R Spitz, Calvin S Carter
{"title":"Protocol to evaluate markers of reactive oxygen species and labile iron from a single sample across in vitro and in in vivo lung cancer models.","authors":"Jennifer A Petsche, Sunny C Huang, Danielle J Foster, Charles C Searby, Val C Sheffield, Douglas R Spitz, Calvin S Carter","doi":"10.1016/j.xpro.2026.104893","DOIUrl":"10.1016/j.xpro.2026.104893","url":null,"abstract":"","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104893"},"PeriodicalIF":1.4,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115841","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 tri-modal pretraining and downstream fine-tuning of protein representations using ProteinAligner. 协议的三模式预训练和下游微调的蛋白质表示使用ProteinAligner。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104862
Han Guo, Li Zhang, Leah Schaffer, Young Su Ko, Digvijay Singh, Hamid Rahmani, Danielle Grotjahn, Elizabeth Villa, Michael Gilson, Wei Wang, Trey Ideker, Eric Xing, Pengtao Xie
{"title":"Protocol for tri-modal pretraining and downstream fine-tuning of protein representations using ProteinAligner.","authors":"Han Guo, Li Zhang, Leah Schaffer, Young Su Ko, Digvijay Singh, Hamid Rahmani, Danielle Grotjahn, Elizabeth Villa, Michael Gilson, Wei Wang, Trey Ideker, Eric Xing, Pengtao Xie","doi":"10.1016/j.xpro.2026.104862","DOIUrl":"10.1016/j.xpro.2026.104862","url":null,"abstract":"<p><p>ProteinAligner integrates protein sequence, three-dimensional structure, and functional annotations in a shared embedding space. Here, we present a protocol for tri-modal pretraining and downstream fine-tuning of protein representations using ProteinAligner. We describe steps for preparing both paired sequence-structure and sequence-text datasets from public protein resources and pretraining ProteinAligner with distributed multimodal learning. We then detail procedures for fine-tuning downstream tasks and evaluating performance. 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":"104862"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115808","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 autophagy-related cellular phenotypes in autophagy-deficient human embryonic stem cell-derived lacrimal gland-like organoids. 分析自噬缺陷的人胚胎干细胞衍生的泪腺样器官中自噬相关细胞表型的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104874
Gamze Kocak, Sovan Sarkar
{"title":"Protocol for analyzing autophagy-related cellular phenotypes in autophagy-deficient human embryonic stem cell-derived lacrimal gland-like organoids.","authors":"Gamze Kocak, Sovan Sarkar","doi":"10.1016/j.xpro.2026.104874","DOIUrl":"10.1016/j.xpro.2026.104874","url":null,"abstract":"<p><p>Autophagy is a vital catabolic process that maintains cellular homeostasis and survival and supports gland tissue development and function. Here, we present a protocol to characterize the cellular phenotypes of autophagy-deficient (ATG5<sup>-/-</sup>) lacrimal gland (LG)-like organoids derived from human embryonic stem cells. We describe steps for organoid cryosectioning, followed by the quantitative assessment of cell death and aggresomes using fluorescence-based TUNEL and ProteoStat staining, respectively, along with pharmacological rescue. This approach enables robust evaluation of autophagy-related cellular dysfunction in human organoid models. For complete details on the use and execution of this protocol, please refer to Kocak et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104874"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115784","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 brain and ventricle volume comparison after clearing and light-sheet microscopy in mice. 清除和薄层显微镜下小鼠脑和脑室体积比较方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104877
Ana Blas-Medina, Minh Son Phan, Samir Ali-Moussa, Nathalie Spassky, Julien Fernandes, Jean-Yves Tinevez, Aleksandra Deczkowska, Laetitia Travier
{"title":"Protocol for brain and ventricle volume comparison after clearing and light-sheet microscopy in mice.","authors":"Ana Blas-Medina, Minh Son Phan, Samir Ali-Moussa, Nathalie Spassky, Julien Fernandes, Jean-Yves Tinevez, Aleksandra Deczkowska, Laetitia Travier","doi":"10.1016/j.xpro.2026.104877","DOIUrl":"10.1016/j.xpro.2026.104877","url":null,"abstract":"<p><p>Analysis of brain and ventricular volumes provides insights into the physiological and pathological progression of brain development and aging, but accessible and cost-effective approaches are lacking. Here, we present a workflow to quantify relative brain and ventricular volumes in unsectioned cleared mouse brains following fluorescent detection of brain tissue and ventricle lining. We describe steps for brain harvesting, clearing, imaging by light-sheet microscopy, image resampling, and ventricle annotation, and comparing brains from adult, neonate, germ-free, and hydrocephalic mouse models.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104877"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115793","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 isolation and quality assessment of extracellular vesicles from bacterial cultures. 细菌培养细胞外囊泡的分离和质量评估方法。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104876
Junhua Xie, Wanyu Zhang, Ze Tao, Shaoping Nie
{"title":"Protocol for isolation and quality assessment of extracellular vesicles from bacterial cultures.","authors":"Junhua Xie, Wanyu Zhang, Ze Tao, Shaoping Nie","doi":"10.1016/j.xpro.2026.104876","DOIUrl":"10.1016/j.xpro.2026.104876","url":null,"abstract":"<p><p>Bacterial extracellular vesicles (bEVs) participate in regulating both intra-bacterial community interactions and bacteria-host cell interactions. Here, we propose a universal and highly reproducible protocol for the extraction of bEVs from bacterial culture. The workflow combines differential centrifugation, ultracentrifugation, and enrichment, allowing efficient impurity removal and bEV enrichment. Nano-flow cytometry (nFCM) characterization of the extracted bEVs further confirmed the efficacy of this approach. For complete details on the use and execution of this protocol, please refer to Xie et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104876"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115757","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 sorting hepatocyte-derived extracellular vesicles from mouse liver tissues using immunomagnetic beads. 使用免疫磁珠从小鼠肝组织中分选肝细胞来源的细胞外囊泡的方案。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104866
Cheng-Han Li, Si-Qi Ying, Qin-Lin Xu, Sheng-Feng Bai, Chen-Xi Zheng, Bing-Dong Sui
{"title":"Protocol for sorting hepatocyte-derived extracellular vesicles from mouse liver tissues using immunomagnetic beads.","authors":"Cheng-Han Li, Si-Qi Ying, Qin-Lin Xu, Sheng-Feng Bai, Chen-Xi Zheng, Bing-Dong Sui","doi":"10.1016/j.xpro.2026.104866","DOIUrl":"10.1016/j.xpro.2026.104866","url":null,"abstract":"<p><p>Here, we present a protocol for isolating total liver tissue-derived extracellular vesicles (LT-EVs) from mouse liver tissue and purifying hepatocyte-derived extracellular vesicles (Hep-EVs) using asialoglycoprotein receptor (ASGPR)-based immunomagnetic sorting. We describe steps for mouse liver perfusion, enzymatic digestion, differential centrifugation, ASGPR labeling, and magnetic-activated cell sorting (MACS)-based enrichment. We then detail procedures for extracellular vesicle (EV) quality control by flow cytometry, nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and western blotting. For complete details on the use and execution of this protocol, please refer to Ying et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104866"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115760","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 imaging and quantitative analysis of yolk vesicle distribution and movement in syncytial Drosophila embryos. 果蝇合胞胚胎卵黄囊泡分布和运动的成像和定量分析方法。
IF 1.4
STAR Protocols Pub Date : 2026-10-01 DOI: 10.1016/j.xpro.2026.104879
Pampa Dey, Sameer Thukral, Amitabha Nandi, Mithun Mitra, Richa Rikhy
{"title":"Protocol for imaging and quantitative analysis of yolk vesicle distribution and movement in syncytial Drosophila embryos.","authors":"Pampa Dey, Sameer Thukral, Amitabha Nandi, Mithun Mitra, Richa Rikhy","doi":"10.1016/j.xpro.2026.104879","DOIUrl":"10.1016/j.xpro.2026.104879","url":null,"abstract":"<p><p>Drosophila embryos use maternally deposited yolk vesicles as their nutritional source during syncytial development. We present a protocol for imaging and quantifying yolk vesicle distribution and movement in mRFP-expressing embryos. We describe steps for imaging the embryo across nuclear division cycles, segmenting nuclei and yolk vesicles, and measuring density and size distribution. We detail procedures for analyzing cortical yolk vesicle movement with nuclei using particle image velocimetry and for quantifying net downward speed using particle tracking and a particle-conservation model. For complete details on the use and execution of this protocol, please refer to Thukral et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104879"},"PeriodicalIF":1.4,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115746","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 correlating in vivo calcium imaging with spatial transcriptomics in the mouse brain. 小鼠脑内钙成像与空间转录组学相关的研究方案。
IF 1.4
STAR Protocols Pub Date : 2026-09-30 DOI: 10.1016/j.xpro.2026.104848
Risa Yamazaki, Mark Eddison, Anja Payne, Yuhan Wang
{"title":"Protocol for correlating in vivo calcium imaging with spatial transcriptomics in the mouse brain.","authors":"Risa Yamazaki, Mark Eddison, Anja Payne, Yuhan Wang","doi":"10.1016/j.xpro.2026.104848","DOIUrl":"10.1016/j.xpro.2026.104848","url":null,"abstract":"<p><p>A central challenge in neuroscience research is to elucidate how distinct neuronal types coordinate to produce complex behaviors, which requires linking the molecular identity of neuronal types with their connectivity and activity in behaving animals. Here, we present a protocol for integrating spatial gene-expression profiling with in vivo calcium imaging in the mouse brain. We describe detailed procedures for tissue recovery after in vivo imaging, multiplexed gene-expression detection, and the computational steps to register these two datasets. For complete details on the use and execution of this protocol, please refer to Yamazaki et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104848"},"PeriodicalIF":1.4,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115735","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 quantification of AAV-CRISPR-mediated hepatic gene editing in mice. aav - crispr介导小鼠肝脏基因编辑的定量方案。
IF 1.4
STAR Protocols Pub Date : 2026-09-29 DOI: 10.1016/j.xpro.2026.104849
Kelsey E Jarrett, Rodrigo Baltazar-Nunez, Chloe Anne Borja, Precious Juvie Calderon, Rochelle W Lai, Angela Cheng, Manasvi Paudel, Gabriella E Rubert, Anthony Suberski, Owen K Traina, Sunny Y Cai, Kalyani Srikanth, William R Lagor, Elizabeth J Tarling, Thomas Q de Aguiar Vallim
{"title":"Protocol for quantification of AAV-CRISPR-mediated hepatic gene editing in mice.","authors":"Kelsey E Jarrett, Rodrigo Baltazar-Nunez, Chloe Anne Borja, Precious Juvie Calderon, Rochelle W Lai, Angela Cheng, Manasvi Paudel, Gabriella E Rubert, Anthony Suberski, Owen K Traina, Sunny Y Cai, Kalyani Srikanth, William R Lagor, Elizabeth J Tarling, Thomas Q de Aguiar Vallim","doi":"10.1016/j.xpro.2026.104849","DOIUrl":"10.1016/j.xpro.2026.104849","url":null,"abstract":"<p><p>Adeno associated viral (AAV) delivery of CRISPR-Cas9 enables efficient, targeted hepatic gene disruption composed of both small insertions and deletions (INDELs) and larger DNA structural variants (DNA-SVs), which are difficult to quantify. Here, we present a protocol for quantifying AAV-CRISPR-mediated gene editing in mice. We describe guide RNA (gRNA) design, plasmid cloning, delivery of AAV-CRISPR to the liver, and execution of liver DNA-editing analysis. This protocol enables quantification of INDELs and DNA-SVs, allowing for validation of gene disruption. For complete details on the use and execution of this protocol, please refer to Chan et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 4","pages":"104849"},"PeriodicalIF":1.4,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13654526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082246","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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