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Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

  • Book
  • © 2016

Overview

Editors:
  1. Ana M. Aransay

    1. Genome Analysis Platform, CIC bioGUNE, Derio, Spain

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    You can also search for this editor in PubMed   Google Scholar

  2. José Luis Lavín Trueba

    1. Genome Analysis Platform, CIC bioGUNE, Derio, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • The main aspects and challenges of the most employed HTS technologies are described in detail including all pros and cons associated with them
  • Sample requirements for each HTS technology supplied
  • Case studies with examples of successful strategies will be analyzed
  • Includes supplementary material: sn.pub/extras

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Table of contents (16 chapters)

  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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Keywords

About this book

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.

Editors and Affiliations

  • Genome Analysis Platform, CIC bioGUNE, Derio, Spain

    Ana M. Aransay, José Luis Lavín Trueba

About the editors

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.

Bibliographic Information

  • Book Title: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing

  • Editors: Ana M. Aransay, José Luis Lavín Trueba

  • DOI: https://doi.org/10.1007/978-3-319-31350-4

  • Publisher: Springer Cham

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: Springer International Publishing Switzerland 2016

  • Hardcover ISBN: 978-3-319-31348-1Published: 09 June 2016

  • Softcover ISBN: 978-3-319-81018-8Published: 30 May 2018

  • eBook ISBN: 978-3-319-31350-4Published: 02 June 2016

  • Edition Number: 1

  • Number of Pages: XI, 399

  • Number of Illustrations: 30 b/w illustrations, 42 illustrations in colour

  • Topics: Human Genetics, Systems Biology, Biostatistics

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