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RNA Mapping [electronic resource]: Methods and Protocols

edited by M. Lucrecia Alvarez, Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, AZ, USA, Mahtab Nourbakhsh, Department of Pharmacy and Biotechnology, German University in Cairo, Berlin, Germany, Department of Plastic Surgery, University Hospital of the RWTH Aachen, Aachen, Germany
Format
EBook; Book; Online
Published
New York : Humana Press, [2014]
Language
English
Series
Methods in Molecular Biology
Springer Protocols
Methods in Molecular Biology (Clifton, N.J.)
Springer Protocols (Series)
ISBN
9781493910618 (alk. paper), 1493910612 (alk. paper), 9781493910625 (eBook), 1493910620 (eBook)
Contents
  • Part I Structural RNA mapping
  • Full-length characterization of transcribed genomic region
  • Rapid mapping of RNA 3 and 5 ends
  • Single nucleotide mapping of RNA 5 and 3 ends
  • Analysis of RNA secondary structure
  • Tertiary structure mapping of the Pri-miRNA miR-17-92
  • In situ hybridization detection of miRNA using LNA [trademark] oligonucleotides
  • Quantification of miRNAs by a simple and specific qPCR method
  • RNA isolation for small RNA next-generation sequencing from acellular biofluids
  • Sequencing small RNA : introduction and data analysis fundamentals
  • Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples
  • MicroRNA profiling in plasma or serum using quantitative RT-PCR
  • MicroRNA profiling of exosomes isolated from biofluids and conditioned media
  • Isolation of urinary exosomes for RNA biomarker discovery using a simple, fast, and highly scalable method
  • Part II Functional RNA mapping
  • Identification of actively translated mRNAs
  • Mapping of internal ribosome entry sites (IRES)
  • Mapping of protein binding RNA elements
  • Purification of RNA-binding proteins
  • De novo approach to classify protein-coding and noncoding transcripts based on sequence composition
  • Computational methods to predict long noncoding RNA functions based on co-expression network
  • MicroRNA biogenesis : dicing assay
  • Faster experimental validation of microRNA targets using cold fusion cloning and a dual firefly-Renilla luciferase reporter assay
  • Experimental validation of predicted mammalian microRNAs of mirtron origin
  • A guide for miRNA target prediction and analysis using web-based applications
  • Tapping microRNA regulation networks through integrated analysis of microRNA-mRNA high-throughput profiles
  • miRWalk database for miRNA-target interactions
  • A schematic workflow for collecting information about the interaction between copy number variants and microRNAs using existing resources
  • SYBR green and TaqMan quantitative PCR arrays : expression profile of genes relevant to a pathway or a disease state
  • Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach.
Description
Mode of access: World wide Web.
Notes
Includes bibliographical references and index.
Series Statement
Methods in molecular biology, 1064-3745 ; 1182
Methods in molecular biology (Clifton, N.J.) ; v. 1182. 1064-3745
Springer protocols (Series) 1949-2448
Copyright Not EvaluatedCopyright Not Evaluated
Technical Details
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    a| Part I Structural RNA mapping -- Full-length characterization of transcribed genomic region -- Rapid mapping of RNA 3 and 5 ends -- Single nucleotide mapping of RNA 5 and 3 ends -- Analysis of RNA secondary structure -- Tertiary structure mapping of the Pri-miRNA miR-17-92 -- In situ hybridization detection of miRNA using LNA [trademark] oligonucleotides -- Quantification of miRNAs by a simple and specific qPCR method -- RNA isolation for small RNA next-generation sequencing from acellular biofluids -- Sequencing small RNA : introduction and data analysis fundamentals -- Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples -- MicroRNA profiling in plasma or serum using quantitative RT-PCR -- MicroRNA profiling of exosomes isolated from biofluids and conditioned media -- Isolation of urinary exosomes for RNA biomarker discovery using a simple, fast, and highly scalable method -- Part II Functional RNA mapping -- Identification of actively translated mRNAs -- Mapping of internal ribosome entry sites (IRES) -- Mapping of protein binding RNA elements -- Purification of RNA-binding proteins -- De novo approach to classify protein-coding and noncoding transcripts based on sequence composition -- Computational methods to predict long noncoding RNA functions based on co-expression network -- MicroRNA biogenesis : dicing assay -- Faster experimental validation of microRNA targets using cold fusion cloning and a dual firefly-Renilla luciferase reporter assay -- Experimental validation of predicted mammalian microRNAs of mirtron origin -- A guide for miRNA target prediction and analysis using web-based applications -- Tapping microRNA regulation networks through integrated analysis of microRNA-mRNA high-throughput profiles -- miRWalk database for miRNA-target interactions -- A schematic workflow for collecting information about the interaction between copy number variants and microRNAs using existing resources -- SYBR green and TaqMan quantitative PCR arrays : expression profile of genes relevant to a pathway or a disease state -- Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach.
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