{"title":"Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.","authors":"Bony De Kumar, Jaya Krishnan","doi":"10.1007/978-1-0716-4322-8_14","DOIUrl":null,"url":null,"abstract":"<p><p>ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2889 ","pages":"193-206"},"PeriodicalIF":0.0000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Methods in molecular biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1007/978-1-0716-4322-8_14","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 0
Abstract
ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.
期刊介绍：
For over 20 years, biological scientists have come to rely on the research protocols and methodologies in the critically acclaimed Methods in Molecular Biology series. The series was the first to introduce the step-by-step protocols approach that has become the standard in all biomedical protocol publishing. Each protocol is provided in readily-reproducible step-by-step fashion, opening with an introductory overview, a list of the materials and reagents needed to complete the experiment, and followed by a detailed procedure that is supported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice.
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