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Full Description
This detailed volume presents a comprehensive methodological guide for the study of chimeric RNAs, from their discovery in high-throughput datasets to their validation in the lab and characterization in biological and clinical contexts. Beginning with chapters dedicated to the identification and characterization of chimeric RNAs using numerous bioinformatic tools, this book continues by covering experimental validation and quantification of chimeric RNAs, methods for chimeric RNA functional and mechanistic studies, and translational application of chimeric RNAs and case studies. Written for the highly successful Methods in Molecular Biology series, chapters generally include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips for troubleshooting and avoiding known pitfalls.
Authoritative and up-to-date, Chimeric RNAs: Methods and Protocols, Second Edition serves as an ideal guide to the practical guidance and conceptual grounding needed to advance your work in this increasingly vital area of study.
Contents
Integrative Chimeric RNA Prediction with FASfuse.- Identification of Cross-Strand Chimeric RNAs with cscMap.- Detection of Chimeric RNAs from RNA-Seq Data with ChiTaRS 8.0: Insights for Liquid Biopsy and Drug Target Identification.- Identifying Read-Through Chimeric RNAs with RTCpredictor.- Computational Prediction of Chimeric RNAs from Long Reads Using CTAT-LR-Fusion.- Assembly of a Full-Length Chimeric RNA Transcriptome.- AtFusionDB: A Comprehensive Database of Fusion Transcripts in Model Plant Arabidopsis thaliana.- Detection and Measurement of Chimeric RNAs by RT-PCR Using Novel RNA Extraction Method.- Mass Spectrometry-Based Validation of Chimeric RNAs.- Validation of Plant Fusion Peptides Using Proteomics Data.- Calculating Relative Chimeric RNA Expression with FusionBlaster.- Ribosome RNA Extraction and RNase R Treatment.- Overexpression of Chimeric RNA by Retroviral Transduction.- Antisense Oligonucleotide-Mediated Chimeric RNA Knockdown.- Knockdown of Chimeric RNA by RNAi.- Bioinformatic Discovery of Tumor-Specific Neoantigens Arising from Chimeric RNAs.- Chimeric RNAs as Novel Neoantigens for Extracellular Vesicles-Based Vaccines Against Cancer.- A Sex-Specific Chimeric RNA in Female Immune Regulation: Case Study.- Fusion RNA Profiling in Cancer: Investigating the Etiology of Fusion-Gene-Associated Cancers and Proposing an Approach to Study Connections Between Biological Samples.- Discovery of a Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction: Case Study.
