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Protocol to determine in vitro lipid-protein interactions using liposome flotation assay. 使用脂质体浮选法测定体外脂质-蛋白相互作用的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104543
Karan Khadayat, Morgan House, Vasudeva Tati, Amit S Joshi
{"title":"Protocol to determine in vitro lipid-protein interactions using liposome flotation assay.","authors":"Karan Khadayat, Morgan House, Vasudeva Tati, Amit S Joshi","doi":"10.1016/j.xpro.2026.104543","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104543","url":null,"abstract":"<p><p>Lipid-protein interactions are crucial for cellular metabolism, transport, and signaling. Here, we present a detailed protocol to determine lipid-protein interactions using purified proteins, commercially available lipids, and a gradient centrifugation-based technique. We show how to make liposomes, test liposome size, form sucrose gradients with liposomes and purified protein, and collect and analyze the fractions after centrifugation. This protocol can determine lipid-protein interactions using a variety of liposome compositions for different proteins. For complete details on the use and execution of this protocol, please refer to House et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104543"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857045","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 identifying cell-type-specific genes associated with disease risk using single-cell eQTL data. 使用单细胞eQTL数据鉴定与疾病风险相关的细胞类型特异性基因的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-06 DOI: 10.1016/j.xpro.2026.104545
Xin Fang, Lijun Bian, Caiwang Yan, Guangfu Jin
{"title":"Protocol for identifying cell-type-specific genes associated with disease risk using single-cell eQTL data.","authors":"Xin Fang, Lijun Bian, Caiwang Yan, Guangfu Jin","doi":"10.1016/j.xpro.2026.104545","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104545","url":null,"abstract":"<p><p>Here, we present a protocol for mapping cell-type-specific cis-acting expression quantitative trait loci (cis-eQTLs) in a target tissue and integrating them with genome-wide association study (GWAS) data. We describe pooled-sample multiplexed sequencing, genotype-based cell demultiplexing, cis-eQTL detection in specific cell types, and integration of single-cell eQTLs with GWAS. This protocol facilitates the identification of candidate risk genes and mechanisms underlying disease susceptibility. For complete details on the use and execution of this protocol, please refer to Bian et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104545"},"PeriodicalIF":1.3,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856805","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 to stain phagocytic macrophages and assess phagocytosis function in phagocytic cells. 吞噬巨噬细胞染色和评估吞噬细胞吞噬功能的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-05 DOI: 10.1016/j.xpro.2026.104530
Mostafa Changaei, Seyed Adnan Kashfi, Sara Soudi, Mohammad Adel Ghiass, Seyed Mahmoud Hashemi
{"title":"Protocol to stain phagocytic macrophages and assess phagocytosis function in phagocytic cells.","authors":"Mostafa Changaei, Seyed Adnan Kashfi, Sara Soudi, Mohammad Adel Ghiass, Seyed Mahmoud Hashemi","doi":"10.1016/j.xpro.2026.104530","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104530","url":null,"abstract":"<p><p>The yeast phagocytosis assay serves as a foundational tool for directly visualizing and quantifying a phagocyte's ability to bind and internalize foreign targets. Here, we present a protocol for analyzing phagocytosis in mouse peritoneal macrophages. We describe steps for yeast staining, phagocytosis of stained yeast, hematoxylin staining of macrophages, and light microscopy imaging. We then detail procedures for phagocytic metric analysis, which are also applicable to any phagocytic cells. This protocol can also be used for time-lapse visualization of phagocytosis.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104530"},"PeriodicalIF":1.3,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843658","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 condensate-based stabilization of gene circuit dynamics under growth-mediated dilution in E. coli. 大肠杆菌生长介导稀释条件下基于凝聚物的基因回路动力学稳定方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-05 DOI: 10.1016/j.xpro.2026.104536
Rong Zhang, Xiao-Jun Tian
{"title":"Protocol for condensate-based stabilization of gene circuit dynamics under growth-mediated dilution in E. coli.","authors":"Rong Zhang, Xiao-Jun Tian","doi":"10.1016/j.xpro.2026.104536","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104536","url":null,"abstract":"<p><p>Growth-mediated dilution can destabilize synthetic gene circuits by reducing intracellular concentrations of key regulatory proteins. Here, we present a protocol that uses liquid-liquid phase separation to buffer dilution of transcription factors and stabilize synthetic gene circuits in E. coli. We describe steps for constructing phase-separating self-activation circuits, characterizing condensate material properties by fluorescence recovery after photobleaching, and imaging of condensate-promoter colocalization. We outline single-cell microscopy and population-level plate reader assays to quantify circuit activation, growth-coupled dilution dynamics, and memory retention. 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 2","pages":"104536"},"PeriodicalIF":1.3,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843713","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 isolating and culturing human monocytes from peripheral blood and measuring intracellular calcium dynamics using Fura-2. 从外周血中分离和培养人单核细胞并使用Fura-2测量细胞内钙动力学的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-04 DOI: 10.1016/j.xpro.2026.104511
Maria F Cano-Abad
{"title":"Protocol for isolating and culturing human monocytes from peripheral blood and measuring intracellular calcium dynamics using Fura-2.","authors":"Maria F Cano-Abad","doi":"10.1016/j.xpro.2026.104511","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104511","url":null,"abstract":"<p><p>Here, we present a protocol for isolating and culturing human monocytes from peripheral blood and measuring intracellular calcium ([Ca<sup>2+</sup>]ᵢ) dynamics using the fluorescent indicator Fura-2 AM. We describe steps for separating peripheral blood mononuclear cells (PBMCs) by density gradient centrifugation and purifying monocytes using magnetic-activated cell sorting (MACS). We then detail procedures for culturing purified monocytes and subjecting them to real-time Ca<sup>2+</sup> imaging to evaluate purinergic receptor activation, particularly P2X7 receptors, and downstream Ca<sup>2+</sup> signaling in primary human monocytes. For complete details on the use and execution of this protocol, please refer to Garrosa-Jiménez et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104511"},"PeriodicalIF":1.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843710","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 cerebrospinal fluid analysis using enrichment-enhanced surface-enhanced Raman spectroscopy and transformer-enabled spectral classification. 使用浓缩增强表面增强拉曼光谱和变压器启用光谱分类的脑脊液分析方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-04 DOI: 10.1016/j.xpro.2026.104538
Zhaoyi Li, Dongjie Zhang, Zhaoyang Cheng, Hanju Zhang, Huandi Li, Lin Shi, Nan Wang, Qi Zeng, Xueli Chen
{"title":"Protocol for cerebrospinal fluid analysis using enrichment-enhanced surface-enhanced Raman spectroscopy and transformer-enabled spectral classification.","authors":"Zhaoyi Li, Dongjie Zhang, Zhaoyang Cheng, Hanju Zhang, Huandi Li, Lin Shi, Nan Wang, Qi Zeng, Xueli Chen","doi":"10.1016/j.xpro.2026.104538","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104538","url":null,"abstract":"<p><p>The rapid detection and precise classification of cerebrospinal fluid in acute leukemia patients constitute a crucial clinical imperative. Here, we present a protocol for cerebrospinal fluid analysis deep learning with enrichment-enhanced surface-enhanced Raman spectroscopy (DL-SERS) detection and transformer-enabled spectral classification. We describe steps for preparing SERS-active materials and samples and acquiring SERS spectral data. We then detail procedures for deep learning-based classification. This protocol enables highly sensitive and efficient identification of acute leukemia patients. 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 2","pages":"104538"},"PeriodicalIF":1.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843653","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
scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data. scPASU：从3' scRNA-seq数据中量化聚腺苷化位点使用和备选聚腺苷化的计算方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-04 DOI: 10.1016/j.xpro.2026.104544
Alexandra Krylova, Ninh B Le, Angela H Ting
{"title":"scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.","authors":"Alexandra Krylova, Ninh B Le, Angela H Ting","doi":"10.1016/j.xpro.2026.104544","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104544","url":null,"abstract":"<p><p>3' single-cell RNA sequencing (scRNA-seq) captures polyadenylation (poly(A)) sites, enabling quantification of site usage per gene and cell. Here, we present scPASU (single-cell poly(A) site usage), a Snakemake workflow for quantifying poly(A) site usage and alternative polyadenylation from 3' scRNA-seq data. We describe steps for building a poly(A) site reference, generating a site-by-cell matrix per sample, and testing alternative polyadenylation (APA) between cell groups. This protocol is configurable for organism- and sample-specific parameters and supports discovery of poly(A) sites. For complete details on the use and execution of this protocol, please refer to Le et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104544"},"PeriodicalIF":1.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843723","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 natural and biomedical image processing in the hypercomplex domain using the 2D orthogonal planes split. 使用二维正交平面分割的超复杂域自然和生物医学图像处理协议。
IF 1.3
STAR Protocols Pub Date : 2026-05-04 DOI: 10.1016/j.xpro.2026.104548
Nektarios A Valous, Eckhard Hitzer, Dragoş Duşe, Rodrigo Rojas Moraleda, Ferdinand Popp, Meggy Suarez-Carmona, Anna Berthel, Ismini Papageorgiou, Carlo Fremd, Alexander Rölle, Christina C Westhoff, Bénédicte Lenoir, Niels Halama, Inka Zörnig, Dirk Jäger
{"title":"Protocol for natural and biomedical image processing in the hypercomplex domain using the 2D orthogonal planes split.","authors":"Nektarios A Valous, Eckhard Hitzer, Dragoş Duşe, Rodrigo Rojas Moraleda, Ferdinand Popp, Meggy Suarez-Carmona, Anna Berthel, Ismini Papageorgiou, Carlo Fremd, Alexander Rölle, Christina C Westhoff, Bénédicte Lenoir, Niels Halama, Inka Zörnig, Dirk Jäger","doi":"10.1016/j.xpro.2026.104548","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104548","url":null,"abstract":"<p><p>We present a protocol for processing natural and biomedical images in the hypercomplex domain. First, the protocol converts images into quaternion matrices. It then applies the 2D orthogonal planes split to perform re-colorization, de-colorization, contrast enhancement, re-staining, and stain separation. Finally, it uses post-processing operations to generate the output. The resulting output supports qualitative assessment and downstream processing in computer vision and computational pathology pipelines. For details and literature comparisons, please refer to Valous et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104548"},"PeriodicalIF":1.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843730","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 the design, conduct, and evaluation of prime editing in human pluripotent stem cells. 人类多能干细胞初始编辑的设计、实施和评估方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-04 DOI: 10.1016/j.xpro.2026.104582
Youjun Wu, Mega Sidharta, Aaron Zhong, Benjamin Persily, Mu Li, Ting Zhou
{"title":"Protocol for the design, conduct, and evaluation of prime editing in human pluripotent stem cells.","authors":"Youjun Wu, Mega Sidharta, Aaron Zhong, Benjamin Persily, Mu Li, Ting Zhou","doi":"10.1016/j.xpro.2026.104582","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104582","url":null,"abstract":"","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104582"},"PeriodicalIF":1.3,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147843662","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 mapping murine myeloid bone marrow progenitors and their differentiation into CD103+ cDC1s and CD301b+ cDC2s. 小鼠髓系骨髓祖细胞定位及其向CD103+ cDC1s和CD301b+ cDC2s分化的方法
IF 1.3
STAR Protocols Pub Date : 2026-05-02 DOI: 10.1016/j.xpro.2026.104508
Damir Vurnek, Giorgi Tchitashvili, Anna Seichter, Tomislav Vuletic, Isabel Heß, Lizi Trapaidze, Lukas Heger, Nounagnon Romaric Tochoedo, Christian H K Lehmann, Bart N Lambrecht, Diana Dudziak, Lukas Amon
{"title":"Protocol for mapping murine myeloid bone marrow progenitors and their differentiation into CD103<sup>+</sup> cDC1s and CD301b<sup>+</sup> cDC2s.","authors":"Damir Vurnek, Giorgi Tchitashvili, Anna Seichter, Tomislav Vuletic, Isabel Heß, Lizi Trapaidze, Lukas Heger, Nounagnon Romaric Tochoedo, Christian H K Lehmann, Bart N Lambrecht, Diana Dudziak, Lukas Amon","doi":"10.1016/j.xpro.2026.104508","DOIUrl":"10.1016/j.xpro.2026.104508","url":null,"abstract":"<p><p>Ex vivo differentiation platforms have a long-standing history for studying dendritic cell (DC) ontogeny and function. Here, we present a protocol for differentiating bona fide DCs from murine bone marrow. We describe steps for bone marrow preparation, followed by ex vivo differentiation of DC subtypes resembling either lymphoid or mucosal tissue DC phenotypes. We then detail procedures for flow cytometric analysis and sorting strategies that facilitate phenotypic and functional studies of murine DC subtypes and/or their bone marrow progenitors. For complete details on the use and execution of this protocol, please refer to Amon et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104508"},"PeriodicalIF":1.3,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13147993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147821726","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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