Titlebook: Enhancer RNAs; Methods and Protocol Ulf Andersson ?rom Book 2017 Springer Science+Business Media New York 2017 long ncRNAs.transcription.ge

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Bioinformatics Pipeline for Transcriptome Sequencing Analysis,

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Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis,

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1064-3745 ucible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls..?. .Authoritative and cutting-edge, .Enhancer RNAs: Methods and Protocols. aims to ensure successful results in this rapidly developing field..978-1-4939-8160-1978-1-4939-4035-6Series ISSN 1064-3745 Series E-ISSN 1940-6029

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https://doi.org/10.1007/978-94-010-2025-1ch takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identified ncRNAs.

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re-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-

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The Philosophy of Science of A. S. Eddingtonion of yet uncharacterized regulatory ncRNAs. In this chapter, we discuss the methodologies currently used to estimate RNA decay and outline an experimental protocol for genome-wide estimation of RNA stability of protein-coding and lncRNAs. This protocol details the transcriptional blockage of cultu

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Cellular Fractionation and Isolation of Chromatin-Associated RNA,ation of cells prior to RNA isolation thus enables the analysis of distinct steps in the lifetime of individual RNA molecules that would be masked in bulk RNA preparations from whole cells. Here, we describe a simple two-step differential centrifugation protocol for the isolation of cytoplasmic, nuc

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Visualization of Enhancer-Derived Noncoding RNA,r-derived long noncoding RNAs (long ncRNAs), including enhancer RNAs (eRNAs), are an important component of enhancer function, their expression has not been broadly analyzed at a single cell level via imaging techniques. This protocol describes a method to image eRNA in single cells by in situ hybri

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UV-RNA Immunoprecipitation (UV-RIP) Protocol in Neurons,ted. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, influencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of