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Gene Expression Analysis

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Nalini Raghavachari

    1. Division of Geriatrics and Clinical Gerontology, National Institute on Aging, Bethesda, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Natàlia Garcia-Reyero

    1. Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods an protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1783)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Overview of Gene Expression Analysis: Transcriptomics

    • Nalini Raghavachari, Natàlia Garcia-Reyero
    Pages 1-6

  3. RNA-Seq and Expression Arrays: Selection Guidelines for Genome-Wide Expression Profiling

    • Jessica Minnier, Nathan D. Pennock, Qiuchen Guo, Pepper Schedin, Christina A. Harrington
    Pages 7-33

  4. A Guide for Designing and Analyzing RNA-Seq Data

    • Aniruddha Chatterjee, Antonio Ahn, Euan J. Rodger, Peter A. Stockwell, Michael R. Eccles
    Pages 35-80

  5. SureSelectXT RNA Direct: A Technique for Expression Analysis Through Sequencing of Target-Enriched FFPE Total RNA

    • Jennifer Carter Jones, Alex P. Siebold, Carolina Becker Livi, Anne Bergstrom Lucas
    Pages 81-104

  6. Simultaneous, Multiplexed Detection of RNA and Protein on the NanoString® nCounter® Platform

    • Sarah Warren
    Pages 105-120

  7. Transcript Profiling Using Long-Read Sequencing Technologies

    • Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis
    Pages 121-147

  8. Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol

    • Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J. Green
    Pages 149-169

  9. MicroRNA Expression Analysis: Next-Generation Sequencing

    • Poching Liu
    Pages 171-183

  10. Identification of Transcriptional Regulators That Bind to Long Noncoding RNAs by RNA Pull-Down and RNA Immunoprecipitation

    • Xiangbo Ruan, Ping Li, Haiming Cao
    Pages 185-191

  11. Single-Cell mRNA-Seq Using the Fluidigm C1 System and Integrated Fluidics Circuits

    • Haibiao Gong, Devin Do, Ramesh Ramakrishnan
    Pages 193-207

  12. Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing

    • Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
    Pages 209-241

  13. Expression Profiling of Differentially Regulated Genes in Fanconi Anemia

    • Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, Rama S. Verma
    Pages 243-258

  14. A Review of Transcriptome Analysis in Pulmonary Vascular Diseases

    • Dustin R. Fraidenburg, Roberto F. Machado
    Pages 259-277

  15. Differential Gene Expression Analysis of Plants

    • Mark Arick II, Chuan-Yu Hsu
    Pages 279-298

  16. High Throughput Sequencing-Based Approaches for Gene Expression Analysis

    • R. Raja Sekhara Reddy, M. V. Ramanujam
    Pages 299-323

  17. Network Analysis of Gene Expression

    • Roby Joehanes
    Pages 325-341

  18. Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe

    • Sushmitha Vallabh, Andrey V. Kartashov, Artem Barski
    Pages 343-360

  19. Bayesian Network to Infer Drug-Induced Apoptosis Circuits from Connectivity Map Data

    • Jiyang Yu, Jose M. Silva
    Pages 361-378

  20. Erratum to: RNA-Seq and Expression Arrays: Selection Guidelines for Genome-Wide Expression Profiling

    • Jessica Minnier, Nathan D. Pennock, Qiuchen Guo, Pepper Schedin, Christina A. Harrington
    Pages E1-E1
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Keywords

About this book

This volume provides experimental and bioinformatics approaches related to different aspects of gene expression analysis. Divided in three sections chapters detail wet-lab protocols, bioinformatics approaches, single-cell gene expression, highly multiplexed amplicon sequencing, multi-omics techniques, and targeted sequencing. 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 tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Gene Expression Analysis: Methods and Protocols aims provide useful information to researchers worldwide.

Editors and Affiliations

  • Division of Geriatrics and Clinical Gerontology, National Institute on Aging, Bethesda, USA

    Nalini Raghavachari

  • Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, USA

    Natàlia Garcia-Reyero

Bibliographic Information

  • Book Title: Gene Expression Analysis

  • Book Subtitle: Methods and Protocols

  • Editors: Nalini Raghavachari, Natàlia Garcia-Reyero

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7834-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-7833-5Published: 17 May 2018

  • Softcover ISBN: 978-1-4939-9299-7Published: 25 July 2019

  • eBook ISBN: 978-1-4939-7834-2Published: 16 May 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 387

  • Number of Illustrations: 12 b/w illustrations, 72 illustrations in colour

  • Topics: Human Genetics

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