Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

1. Front Matter

   Pages i-xi

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2. The High-Throughput Sequencing Technologies Triple-W Discussion: Why Use HTS, What Is the Optimal HTS Method to Use, and Which Data Analysis Workflow to Follow

   • José Luis Lavín Trueba, Ana M. Aransay

   Pages 1-12

3. Whole-Genome Sequencing Recommendations

   • Toni Gabaldón, Tyler S. Alioto

   Pages 13-41

4. Targeted DNA Region Re-sequencing

   • Karolina Heyduk, Jessica D. Stephens, Brant C. Faircloth, Travis C. Glenn

   Pages 43-68

5. Transcriptome Profiling Strategies

   • Abdullah M. Khamis, Vladimir B. Bajic, Matthias Harbers

   Pages 69-104

6. Differential mRNA Alternative Splicing

   • Albert Lahat, Sushma Nagaraja Grellscheid

   Pages 105-119

7. microRNA Discovery and Expression Analysis in Animals

   • Bastian Fromm

   Pages 121-142

8. Analysis of Long Noncoding RNAs in RNA-Seq Data

   • Farshad Niazi, Saba Valadkhan

   Pages 143-174

9. Ribosome Profiling

   • Anze Zupanic, Sushma Nagaraja Grellscheid

   Pages 175-195

10. Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing

    • Tuncay Baubec, Altuna Akalin

    Pages 197-221

11. Characterization of DNA-Protein Interactions: Design and Analysis of ChIP-Seq Experiments

    • Rory Stark, James Hadfield

    Pages 223-260

12. PAR-CLIP: A Genomic Technique to Dissect RNA-Protein Interactions

    • Tara Dutka, Aishe A. Sarshad, Markus Hafner

    Pages 261-289

13. Metagenomic Design and Sequencing

    • William L. Trimble, Stephanie M. Greenwald, Sarah Owens, Elizabeth M. Glass, Folker Meyer

    Pages 291-312

14. A Hitchhiker’s Guide to Metatranscriptomics

    • Mariana Peimbert, Luis David Alcaraz

    Pages 313-342

15. Eukaryotic Single-Cell mRNA Sequencing

    • Kenneth J. Livak

    Pages 343-365

16. Eukaryotic Single-Cell DNA Sequencing

    • Keith E. Szulwach, Kenneth J. Livak

    Pages 367-384

17. Submitting Data to a Public Repository, the Final Step of a Successful HTS Experiment

    • Christopher O’Sullivan, Jonathan Trow

    Pages 385-391

18. Back Matter

    Pages 393-399

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High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.

• Bioinformatics
• DNA
• Epigenetics
• Genetics
• Genomics
• HTS
• Systems Biology

• Genome Analysis Platform, CIC bioGUNE, Derio, Spain

  Ana M. Aransay, José Luis Lavín Trueba

Ana M. Aransay received her B.Sc. in Biology from the University of the Basque Country in 1992. She completed her Ph.D. in Medicine at University of Crete, Greece. After receiving her PhD in 1999, she obtained two consecutive post-doctoral research grants from the Basque Country Government to carry out a project on population genetics of vectors of parasitic diseases. Since November 2004, she is responsible for the Genome Analysis Platform at CIC bioGUNE, Derio, Spain where the main objectives are to set up state-of-the-art high throughput technologies in order to characterization of genomes from different points of view. Dr. Aransay has authored many articles and was a co-editor on the book “Bioinformatics for High Throughput Sequencing” published by Springer International Publishing in 2012.

José Luis Lavín Trueba, received two B.Sc., in Biology (1999) and Biochemistry (2000) from the University of Salamanca. For his Ph.D. studies, he became interested in bioinformatics and received his Ph.D. on this discipline at the Dept. of Genetics and Microbiology at the Public University of Navarre in 2008. He has worked in different fields of Bioinformatics (Comparative genomics, Genome Annotation, Promoter sequences analysis and Secreted proteins analysis). During his studies, he also became proficient in some programming languages such as Perl/CGI, MySQL, HTML/CSS, Python or R, which allowed him to develop online biological databases and bioinformatic tools. As a result of this work, he has collaborated in several genome sequencing projects as part of international sequencing consortiums. During 2012, he entered the Next Generation Sequencing data analysis field, working as Platform Specialist in bioinformatics for the Genome Analysis Platform at CIC bioGUNE, Derio, Spain, where he analyzes data from a wide variety of sources (microarray and HTS technologies included) and is also actively designing and developing web tools aimed to enhance the use of bioinformatic analysis pipelines for neophytes.

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