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Protocol for genetic analysis of population-scale ultra-low-depth sequencing data. 群体规模的超低深度测序数据的遗传分析方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-16 DOI: 10.1016/j.xpro.2024.103579
Jingyu Zeng, Linxuan Li, Ying Lin, Xianmei Lan, Xinyi Zhang, Yingying Wang, Mingzhi Liao, Xin Jin, Huanhuan Zhu
{"title":"Protocol for genetic analysis of population-scale ultra-low-depth sequencing data.","authors":"Jingyu Zeng, Linxuan Li, Ying Lin, Xianmei Lan, Xinyi Zhang, Yingying Wang, Mingzhi Liao, Xin Jin, Huanhuan Zhu","doi":"10.1016/j.xpro.2024.103579","DOIUrl":"10.1016/j.xpro.2024.103579","url":null,"abstract":"<p><p>Non-invasive prenatal testing (NIPT) not only enables the detection of chromosomal anomalies in fetuses but also generates vast amounts of ultra-low-depth sequencing data, which can be leveraged for population genomic studies. Here, we present a protocol designed for massive ultra-low-depth sequencing datasets. We detail the steps for data processing, quality control, and genotype imputation, followed by genome-wide association study (GWAS) and post-GWAS analyses. This protocol applies to a wide range of ultra-low-depth sequencing studies, extending beyond data from NIPT. For complete details on the use and execution of this profile, please refer to Xiao et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103579"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11787503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013065","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 infer off-target effects of drugs on cellular signaling using interactome-based deep learning. 使用基于相互作用组的深度学习来推断药物对细胞信号传导的脱靶效应的协议。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-16 DOI: 10.1016/j.xpro.2024.103573
Nikolaos Meimetis, Douglas A Lauffenburger, Avlant Nilsson
{"title":"Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.","authors":"Nikolaos Meimetis, Douglas A Lauffenburger, Avlant Nilsson","doi":"10.1016/j.xpro.2024.103573","DOIUrl":"10.1016/j.xpro.2024.103573","url":null,"abstract":"<p><p>Drugs that target specific proteins often have off-target effects. We present a protocol using artificial neural networks to model cellular transcriptional responses to drugs, aiming to understand their mechanisms of action. We detail steps for predicting transcriptional activities, inferring drug-target interactions, and explaining the off-target mechanism of action. As a case study, we analyze the off-target effects of lestaurtinib on FOXM1 in the A375 cell line. For complete details on the use and execution of this protocol, please refer to Meimetis et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103573"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013090","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 transcription factor target genes using TargetOrtho2.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-03-06 DOI: 10.1016/j.xpro.2025.103680
Jonathan D Rumley, Jee Hun Kim, Oliver Hobert
{"title":"Protocol to identify transcription factor target genes using TargetOrtho2.","authors":"Jonathan D Rumley, Jee Hun Kim, Oliver Hobert","doi":"10.1016/j.xpro.2025.103680","DOIUrl":"10.1016/j.xpro.2025.103680","url":null,"abstract":"<p><p>TargetOrtho2 uses transcription factor binding site information to predict transcription factor targets in C. elegans, based on an in silico phylogenetic footprinting approach. Here, we present a protocol to identify transcription factor target genes using a new version of TargetOrtho2. We provide instructions for installing TargetOrtho2 and its required suite of programs, for predicting transcription factor target genes, and for updating and adding new genomes to TargetOrtho2.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103680"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11930065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582379","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 isolation of silk glands from silkworms for snRNA-seq and spatial transcriptomics. 家蚕丝腺分离snRNA-seq和空间转录组学研究方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-12 DOI: 10.1016/j.xpro.2024.103581
Yan Ma, Keshu Dong, Jie Hu, Yiyun Tang, Hanfu Xu
{"title":"Protocol for the isolation of silk glands from silkworms for snRNA-seq and spatial transcriptomics.","authors":"Yan Ma, Keshu Dong, Jie Hu, Yiyun Tang, Hanfu Xu","doi":"10.1016/j.xpro.2024.103581","DOIUrl":"10.1016/j.xpro.2024.103581","url":null,"abstract":"<p><p>The silk glands (SGs) of silkworms specifically synthesize silk proteins, thus strongly influencing the yield and quality of silk. Here, we present a protocol for isolating SG nuclei from silkworms and obtaining high-quality tissue slices for spatial transcriptomics. We describe steps for rearing, dissecting, and nucleus isolation. We then detail procedures for embedding, frozen section, and RNA capturing and sequencing. This protocol enables the exploration of the spatial distribution of SG cells at single-cell resolution. For complete details on the use and execution of this protocol, please refer to Ma et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103581"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11772954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980213","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 identifying Dicer as dsRNA binding and cleaving reagent in response to transfected dsRNA. 根据转染的 dsRNA 确定 Dicer 作为 dsRNA 结合和裂解试剂的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-24 DOI: 10.1016/j.xpro.2024.103591
Yunpeng Dai, Jiaxin Wang, Jiaqi Zhang, Xing Liu, Gang Sun, Jinfeng Lu, Yang Li
{"title":"Protocol for identifying Dicer as dsRNA binding and cleaving reagent in response to transfected dsRNA.","authors":"Yunpeng Dai, Jiaxin Wang, Jiaqi Zhang, Xing Liu, Gang Sun, Jinfeng Lu, Yang Li","doi":"10.1016/j.xpro.2024.103591","DOIUrl":"10.1016/j.xpro.2024.103591","url":null,"abstract":"<p><p>Mammalian Dicer has been proved to be functional on double-stranded RNAs (dsRNAs) and involved in antiviral immunity or immune regulation. Here, we present a protocol for identifying Dicer as a dsRNA binding and cleaving factor to transfected dsRNA in cell lines, based on small RNA sequencing (RNA-seq) and dsRNA-immunoprecipitation (dsRNA-IP). We detail both experimental processes and analysis on small RNA-seq data. This protocol can be further applied to identify proteins that process dsRNA into small RNAs, like RNase L. For complete details on the use and execution of this protocol, please refer to Dai et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103591"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11804107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143042079","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 quantitative detection of mtDNA in the supernatants of activated human naive CD8+ T cells.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-01-31 DOI: 10.1016/j.xpro.2025.103612
Linlin Li, Jun Jin
{"title":"Protocol for the quantitative detection of mtDNA in the supernatants of activated human naive CD8<sup>+</sup> T cells.","authors":"Linlin Li, Jun Jin","doi":"10.1016/j.xpro.2025.103612","DOIUrl":"10.1016/j.xpro.2025.103612","url":null,"abstract":"<p><p>Here, we present a protocol for the quantitative characterization of human T cell aging. We describe steps for sample collection; peripheral blood mononuclear cell (PBMC) isolation; and the enrichment, assessment, and activation of naive CD8<sup>+</sup> T cells. We then detail procedures for supernatant collection and quantification using the absolute copy number of mitochondrial DNA (mtDNA) released into the supernatants from in-vitro-activated naive CD8<sup>+</sup> T cells. We also apply this approach to predict the occurrence of lung adenocarcinoma in middle-aged populations. For complete details on the use and execution of this protocol, please refer to Jin et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103612"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075713","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 perfusing human axillary lymph nodes ex vivo to study structure and function in real time.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-05 DOI: 10.1016/j.xpro.2025.103624
Amy Llewellyn, Rachel Barrow-McGee, Julia Stevenson, Jasmine Gore, Kalnisha Naidoo
{"title":"Protocol for perfusing human axillary lymph nodes ex vivo to study structure and function in real time.","authors":"Amy Llewellyn, Rachel Barrow-McGee, Julia Stevenson, Jasmine Gore, Kalnisha Naidoo","doi":"10.1016/j.xpro.2025.103624","DOIUrl":"10.1016/j.xpro.2025.103624","url":null,"abstract":"<p><p>Lymph nodes regulate immunity and maintain fluid balance in health and disease. Here, we present a protocol that uses normothermic perfusion to sustain patient-derived lymph nodes ex vivo for up to 24 h to study their structure and function. We describe steps for setting up both thermoregulatory and perfusion circuits, cannulating human lymph nodes, and perfusion. This protocol can be used to study how human lymph nodes change in cancer and other diseases, and/or in response to perturbations, including drugs. For complete details on the use and execution of this protocol, please refer to Barrow-McGee et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103624"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366015","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 automated tracking and quantification of adult zebrafish anxiety behavior using ZebraTrack.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-10 DOI: 10.1016/j.xpro.2025.103631
Atanu Pramanik, Shubham Nema, Yogesh Bhargava, Anamika Bhargava
{"title":"Protocol for automated tracking and quantification of adult zebrafish anxiety behavior using ZebraTrack.","authors":"Atanu Pramanik, Shubham Nema, Yogesh Bhargava, Anamika Bhargava","doi":"10.1016/j.xpro.2025.103631","DOIUrl":"10.1016/j.xpro.2025.103631","url":null,"abstract":"<p><p>The open-field tank test is a well-validated technique for evaluating anxiety behavior in vertebrate animal models. However, manual behavioral analysis can be subjective and time consuming. Here, we present a protocol using ZebraTrack, an open-source ImageJ-based approach for distraction-free swimming video acquisition and automated tracking of adult zebrafish. We detail steps for mathematical calculations on 2D coordinates to extract various behavioral endpoints for anxiety-behavioral evaluation. For complete details on the use and execution of this protocol, please refer to Nema et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103631"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399946","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 creation and utilization of 3D pancreatic cancer models from circulating tumor cells. 利用循环肿瘤细胞创建和利用三维胰腺癌模型的方案。
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-11 DOI: 10.1016/j.xpro.2025.103635
Jiajia Tang, Quan Zheng, Qi Wang, Yaru Zhao, Preeta Ananthanarayanan, Chiara Reina, Berina Šabanović, Ke Jiang, Ming-Hsin Yang, Clara Csilla Meny, Huimin Wang, Mette Ø Agerbaek, Thomas Mandel Clausen, Tobias Gustavsson, Chenlei Wen, Felice Borghi, Alfredo Mellano, Elisabetta Fenocchio, Vanesa Gregorc, Anna Sapino, Thor G Theander, Da Fu, Alexandra Aicher, Ali Salanti, Baiyong Shen, Christopher Heeschen
{"title":"Protocol for the creation and utilization of 3D pancreatic cancer models from circulating tumor cells.","authors":"Jiajia Tang, Quan Zheng, Qi Wang, Yaru Zhao, Preeta Ananthanarayanan, Chiara Reina, Berina Šabanović, Ke Jiang, Ming-Hsin Yang, Clara Csilla Meny, Huimin Wang, Mette Ø Agerbaek, Thomas Mandel Clausen, Tobias Gustavsson, Chenlei Wen, Felice Borghi, Alfredo Mellano, Elisabetta Fenocchio, Vanesa Gregorc, Anna Sapino, Thor G Theander, Da Fu, Alexandra Aicher, Ali Salanti, Baiyong Shen, Christopher Heeschen","doi":"10.1016/j.xpro.2025.103635","DOIUrl":"10.1016/j.xpro.2025.103635","url":null,"abstract":"<p><p>We introduce a protocol for generating 3D organoids from circulating tumor cells (CTCs), enabling longitudinal functional and molecular analyses in pancreatic cancer patients, including those with unresectable disease, which constitutes the majority of cases. We outline the process for isolating and characterizing CTCs from the blood of pancreatic cancer patients and provide detailed instructions for initiating, passaging, and phenotyping CTC-derived organoids. Additionally, we describe techniques for utilizing these organoids in drug screening with a focus on stemness-related pathways. For complete details on the use and execution of this protocol, please refer to Tang et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103635"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11870243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143415414","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 AI-based segmentation and quantification of interstitial cells of Cajal in murine gastric muscle.
IF 1.3
STAR Protocols Pub Date : 2025-03-21 Epub Date: 2025-02-19 DOI: 10.1016/j.xpro.2025.103644
Egan L Choi, Negar Taheri, Yujiro Hayashi
{"title":"Protocol for AI-based segmentation and quantification of interstitial cells of Cajal in murine gastric muscle.","authors":"Egan L Choi, Negar Taheri, Yujiro Hayashi","doi":"10.1016/j.xpro.2025.103644","DOIUrl":"10.1016/j.xpro.2025.103644","url":null,"abstract":"<p><p>Interstitial cells of Cajal (ICCs), pacemaker and neuromodulator cells in the gastrointestinal (GI) tract, play an important role in GI motility. However, quantifying ICCs is challenging due to their mixed morphologies. Here, we present a protocol for preparing and immunostaining ICC in the murine gastric tunica muscularis using artificial intelligence (AI). We describe steps for obtaining muscles, whole-mount staining, and imaging ICC using confocal microscope. We then detail procedures for training an AI to identify ICCs and quantify their volume. For complete details on the use and execution of this protocol, please refer to Taheri et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103644"},"PeriodicalIF":1.3,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469464","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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