{"title":"对末端模式流式细胞测序基因表达的直接cDNA cap分析方案。","authors":"Diane Delobel, Hiromi Nishiyori-Sueki, Ilaria Nisoli, Hideya Kawaji, Pauline Robbe, Piero Carninci, Hazuki Takahashi","doi":"10.1016/j.xpro.2024.103594","DOIUrl":null,"url":null,"abstract":"<p><p>Cap analysis of gene expression (CAGE) is a technique that facilitates the assessment of the 5'-end of RNA transcript starting site (TSS) of both coding and non-coding genes. Here, we present a protocol for using CAGE on Illumina patterned flow cell technology with dual indexes on mouse and human samples. We describe steps for sequencing, automated data processing, and complete analytical framework ensuring CAGE operability for the determination of TSS and enhancers on the ever-evolving Illumina sequencing platforms.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"6 1","pages":"103594"},"PeriodicalIF":1.3000,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851279/pdf/","citationCount":"0","resultStr":"{\"title\":\"Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing.\",\"authors\":\"Diane Delobel, Hiromi Nishiyori-Sueki, Ilaria Nisoli, Hideya Kawaji, Pauline Robbe, Piero Carninci, Hazuki Takahashi\",\"doi\":\"10.1016/j.xpro.2024.103594\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Cap analysis of gene expression (CAGE) is a technique that facilitates the assessment of the 5'-end of RNA transcript starting site (TSS) of both coding and non-coding genes. Here, we present a protocol for using CAGE on Illumina patterned flow cell technology with dual indexes on mouse and human samples. We describe steps for sequencing, automated data processing, and complete analytical framework ensuring CAGE operability for the determination of TSS and enhancers on the ever-evolving Illumina sequencing platforms.</p>\",\"PeriodicalId\":34214,\"journal\":{\"name\":\"STAR Protocols\",\"volume\":\"6 1\",\"pages\":\"103594\"},\"PeriodicalIF\":1.3000,\"publicationDate\":\"2025-03-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851279/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"STAR Protocols\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1016/j.xpro.2024.103594\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/2/6 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"STAR Protocols","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.xpro.2024.103594","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/2/6 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing.
Cap analysis of gene expression (CAGE) is a technique that facilitates the assessment of the 5'-end of RNA transcript starting site (TSS) of both coding and non-coding genes. Here, we present a protocol for using CAGE on Illumina patterned flow cell technology with dual indexes on mouse and human samples. We describe steps for sequencing, automated data processing, and complete analytical framework ensuring CAGE operability for the determination of TSS and enhancers on the ever-evolving Illumina sequencing platforms.
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