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Tiling Arrays

Methods and Protocols

  • Book
  • © 2013

Overview

Editors:
  1. Tin-Lap Lee

    1. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

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  2. Alfred Chun Shui Luk

    1. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

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  • Focuses on key application of tiling microarrays in genomic discovery
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1067)

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Table of contents (14 protocols)

  1. Front Matter

    Pages i-xi
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  2. Overview

    1. Front Matter

      Pages 1-1
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    2. A Brief Introduction to Tiling Microarrays: Principles, Concepts, and Applications

      • Christophe Lemetre, Zhengdong D. Zhang
      Pages 3-19

  3. Transcriptional Regulation and Expression

    1. Front Matter

      Pages 21-21
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    2. Design of Tiling Arrays and Their Application to Bacterial Transcriptome Analysis

      • Takeshi Akama, Kazuaki Nakamura, Akito Tanoue, Koichi Suzuki
      Pages 23-34

    3. Transcript Profiling in Arabidopsis with Genome Tiling Microarrays

      • Diana Coman, Wilhelm Gruissem, Lars Hennig
      Pages 35-49

    4. Genome-Wide Analysis of Transcription Factor-Binding Sites in Skeletal Muscle Cells Using ChIP-Seq

      • Chung-II An, Nobuko Hagiwara
      Pages 51-64

    5. Analysis of Allele-Specific Gene Expression Using a Target-Oriented Tiling Microarray Assay

      • Huiyong Zhang, Xing-Wang Deng, Lei Li
      Pages 65-76

  4. Genetics and Epigenetics Regulation

    1. Front Matter

      Pages 77-77
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    2. Detection of Epigenetic Alterations Using Tiling Arrays

      • Hoi-Hung Cheung, Owen M. Rennert, Tin-Lap Lee
      Pages 79-86

    3. Investigating Gene Promoter Methylation in a Mouse Model of Status Epilepticus

      • Suzanne F. C. Miller-Delaney, Sudipto Das, Raymond L. Stallings, David C. Henshall
      Pages 87-101

  5. Data Analysis

    1. Front Matter

      Pages 103-103
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    2. Integrative Analysis of ChIP-Chip and ChIP-Seq Dataset

      • Lihua Julie Zhu
      Pages 105-124

    3. HAT: A Novel Statistical Approach to Discover Functional Regions in the Genome

      • Erdogan Taskesen, Bas Wouters, Ruud Delwel
      Pages 125-141

    4. Inference of Alternative Splicing from Tiling Array Data

      • Johannes Eichner
      Pages 143-164

    5. Analysis of In Vivo Occupancy of Aebp1, a Transcription Factor, Using High Resolution Tiling Array

      • Swati Sinha, Sainitin Donakonda, Satyanarayana MR Rao
      Pages 165-183

    6. Application of the Simple and Efficient Mpeak Modeling in Binding Peak Identification in ChIP-Chip Studies

      • Ming Zheng, Yunmin Li, Yun-Fai Chris Lau
      Pages 185-202

    7. Evaluation of MeDIP-Chip in the Context of Whole-Genome Bisulfite Sequencing (WGBS-Seq) in Arabidopsis

      • René Wardenaar, Haiyin Liu, Vincent Colot, Maria Colomé-Tatché, Frank Johannes
      Pages 203-224

    8. Mapping Genomic Features of Tiling Microarray Data by TileMapper

      • Hoi-Hung Cheung, Janek Claus, Sumeeta Singh, Chandan Sastry, Owen M. Rennert, Wai-Yee Chan et al.
      Pages 225-233

  6. Back Matter

    Pages 235-236
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Keywords

About this book

 In Tiling Arrays: Methods and Protocols,  expert researchers in the field detail many of the methods which are now commonly used to study tiling microarrays in genomic discovery . These include methods and applications for transcriptional regulation, expression, genetic and epigenetic regulation, as well as techniques and skills on tiling microarray data analysis. 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, Tiling Arrays: Methods and Protocols  seeks to provide scientists with a comprehensive and down to earth approach to maximize results.

Editors and Affiliations

  • Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Tin-Lap Lee, Alfred Chun Shui Luk

Bibliographic Information

  • Book Title: Tiling Arrays

  • Book Subtitle: Methods and Protocols

  • Editors: Tin-Lap Lee, Alfred Chun Shui Luk

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-607-8

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2013

  • Hardcover ISBN: 978-1-62703-606-1Published: 24 August 2013

  • Softcover ISBN: 978-1-4939-5992-1Published: 23 August 2016

  • eBook ISBN: 978-1-62703-607-8Published: 24 August 2013

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 236

  • Number of Illustrations: 16 b/w illustrations, 37 illustrations in colour

  • Topics: Human Genetics, Microarrays

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