Main description:

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.

Contents:

Part I: OverView

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

Christophe Lemetre and Zhengdong D. Zhang

Part II: Transcriptional Regulation and Expression

2. Design of Tiling Arrays and their Application to Bacterial Transcriptome Analysis

Takeshi Akama, Kazuaki Nakamura, Akito Tanoue, and Koichi Suzuki

3. Transcript Profiling in Arabidopsis with Genome Tiling Microarrays

Diana Coman, Wilhelm Gruissem, and Lars Hennig

4. Genome-wide Analysis of Transcription Factor Binding Sites in Skeletal Muscle Cells using ChIP-seq

Chung-Il An and Nobuko Hagiwara

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

Huiyong Zhang, Xing-Wang Deng, and Lei Li

Part III: Genetics and Epigenetics Regulation

6. Detection of Epigenetic Alterations Using Tiling Arrays

Hoi-Hung Cheung and Owen M Rennert

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

Suzanne F. C. Miller-Delaney, Sudipto Das, Raymond L. Stallings, and David C. Henshall

Part IV: Data Analysis

8. Integrative Analysis of ChIP-chip and ChIP-seq Dataset

Lihua Julie Zhu

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

Erdogan Taskesen, Bas Wouters, and Ruud Delwel

10. Inference of Alternative Splicing from Tiling Array Data

Johannes Eichner

11. Analysis of in vivo Occupancy of Aebp1, a Transcription Factor, using High Resolution Tiling ArraySwati Sinha, Sainitin Donakonda, and Satyanarayana MR Rao

12. Application of the Simple and Efficient MPeak Modeling in Binding Peak Identification in CHIP-CHIP Studies

Ming Zheng, Yunmin Li, and Yun-Fai Chris Lau

13. Evaluation of MeDIP-chip in the Context of Whole Genome Bisulphite Sequencing (WGBS-seq) in Arabidopsis

Rene Wardenaar, Haiyin Liu, Vincent Colot, Maria Colome-Tatche, Frank Johannes

14. Mapping Genomic Features of Tiling Microarray Data by TileMapper

Hoi-Hung Cheung, Janek Claus, Sumeeta Singh, Chandan Sastry, Owen M Rennert, Wai-Yee Chan, Tin-Lap Lee