RNA Mapping: Methods and Protocols

ISBN-13: 9781493953868 / Angielski / Miękka / 2016 / 375 str.

M. Lucrecia Alvarez; Mahtab Nourbakhsh

Opis

In RNA Mapping- Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study RNA. These include protocols for the consequence of the emerging interest in the characterization of cellular RNAs urged by their potential use as diagnostic biomarkers or therapeutic targets. In particular, the biological relevance of microRNAs in human physiology and disease development is highlighted in the 16 chapters focused on methods for their physical and functional mapping. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.Authoritative and practical, RNA Mapping- Methods and Protocols provides instruction and inspiration for scientists who are facing the challenges of the discovery and/or functional characterization of RNA molecules for a wide variety of applications ranging from novel biomedical diagnostics to therapeutics and biomaterials.

Spis treści

Part I-Structural RNA Mapping

1.      Full-Length Characterization Of Transcribed Genomic Regions

Marc René Reboll, M. Lucrecia Alvarez, and Mahtab Nourbakhsh

 

2.      Rapid Mapping Of RNA 3´and 5´Ends

Victoria Zismann and Mahtab Nourbakhsh

 

3.      Single Nucleotide Mapping Of RNA 5´and 3´Ends

Mahtab Nourbakhsh

 

4.      RNA Secondary Structure Analysis

Mahtab  Nourbakhsh

 

5.      Tertiary Structure Mapping Of Pri-Mirna17~92

Steven G. Chaulk and Richard P. Fahlman

 

6.      In Situ Hybridization Detection Of Micrornas Using LNA Oligonucleotides

Olga Beltcheva and Stefania Cotta Done

 

7.      Quantification Of Micrornas By A Simple And Specific Qpcr Method

Peter Busk and Susanna Cirera

 

8.      RNA Isolation For Small RNA Next Generation Sequencing From Acellular Biofluids

Kasandra L. Burgos and Kendall Van Keuren-Jensen

 

9.      Sequencing Small RNA: Introduction and Data Analysis Fundamentals

Jai Prakash Mehta

 

10.  Measuring Expression Levels Of Small Regulatory RNA Molecules From Formalin-Fixed, Paraffin-Embedded Samples and Body Fluids

Adrienn Gyongyosi, Otto Docs, Zsolt Czimmerer, Laszlo Orosz, Attila Horvath, Olga Török, Gabor Mehes, Laszlo Nagy, and Balint L Balint

 

11.  Microrna Profiling In Plasma Or Serum Using Quantitative RT-Qpcr

Marina C. Costa, Ana Lúcia Leitão, and Francisco J. Enguita

 

12.  Microrna Profiling Of Exosomes Isolated From Biofluids And Conditioned Media

Sweta Rani

 

13.  Isolation Of Urinary Exosomes For RNA Biomarker Discovery Using A Simple, Fast, And Highly Scalable Method

M. Lucrecia Alvarez

Part II- Functional RNA Mapping

14.  Identification Of Actively Translated Mrnas

Marc René Reboll and Mahtab Nourbakhsh

 

15.  Mapping Of Internal Ribosome Entry Sites (IRES)

Sarah Mehrtens and Marc René Reboll

 

16.  Mapping Of Protein Binding RNA Elements

Marc René Reboll

 

17.  Purification Of RNA Binding Proteins

Birgit Ritter and Marc René Reboll

 

18.  De Novo Approach To Classify Protein-Coding And Non-Coding Transcripts By Utilizing Sequence Intrinsic Composition

Haitao Luo, Dechao Bu, Liang Sun, and Yi Zhao

 

19.  Computational Methods To Predict Long Non-Coding RNA Functions Based On Co-Expression Network

Yi Zhao, Haitao Luo, Xiaowei Chen, Yi Xiao, and Runsheng Chen

 

20.  Microrna Biogenesis - Dicing Assay

Carlos A. Melo and Sonia A. Melo

 

21.  Faster Experimental Validation Of Microrna Targets Using Cold Fusion Cloning And A Dual Firefly-Renilla Luciferase Reporter Assay

M. Lucrecia Alvarez

 

22.  Experimental Validation Of Predicted Mammalian Micrornas Of Mirtron Origin

Anita Schamberger and Tamás I. Orbán

 

23.  A Guide For Microrna Target Prediction And Analysis Using Web-Based Applications

Ana Lúcia Leitão, Marina C. Costa, and Francisco J. Enguita

 

24.  Tapping Microrna Regulation Networks Through Integrated Analysis Of Microrna-Mrna High-Throughput Profiles

Anthony D. Saleh and Hui Cheng

 

25.  Mirwalk Database For Microrna-Target Interactions

Harsh Dweep, Norbert Gretz And Carsten Sticht

26.  A Schematic Workflow For Collecting The Interaction Information Between Copy Number Variants And Micrornas Using Existing Resources

Harsh Dweep, Norbert Gretz,  and Kyriakos Felekkis

 

27.  SYBR Green and Taqman PCR Arrays: Expression Profile Of Genes Relevant To A Pathway Or Disease State

M. Lucrecia Alvarez And Stefania Cotta Done

 

28.  Comprehensive Meta-Analysis Of Microrna Expression Using A Robust Rank Aggregation Approach

Urmo Võsa, Raivo Kolde, Jaak Vilo, Andres Metspalu, and Tarmo Annilo