Introduction to sequencing the brain transcriptome

Robert Hitzemann, Priscila Darakjian, Nikki Walter, Ovidiu Dan Iancu, Robert Searles, Shannon McWeeney

    Research output: Chapter in Book/Report/Conference proceedingChapter

    16 Scopus citations

    Abstract

    High-throughput next-generation sequencing is now entering its second decade. However, it was not until 2008 that the first report of sequencing the brain transcriptome appeared (Mortazavi, Williams, Mccue, Schaeffer, & Wold, 2008). These authors compared short-read RNA-Seq data for mouse whole brain with microarray results for the same sample and noted both the advantages and disadvantages of the RNA-Seq approach. While RNA-Seq provided exon level resolution, the majority of the reads were provided by a small proportion of highly expressed genes and the data analysis was exceedingly complex. Over the past 6 years, there have been substantial improvements in both RNA-Seq technology and data analysis. This volume contains 11 chapters that detail various aspects of sequencing the brain transcriptome. Some of the chapters are very methods driven, while others focus on the use of RNA-Seq to study such diverse areas as development, schizophrenia, and drug abuse. This chapter briefly reviews the transition from microarrays to RNA-Seq as the preferred method for analyzing the brain transcriptome. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, and can be used to extract genotype information, e.g., nonsynonymous coding single nucleotide polymorphisms. RNA-Seq embraces the complexity of the brain transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain-behavior-disease relationships is substantial.

    Original languageEnglish (US)
    Title of host publicationInternational Review of Neurobiology
    PublisherAcademic Press Inc.
    Pages1-19
    Number of pages19
    DOIs
    StatePublished - 2014

    Publication series

    NameInternational Review of Neurobiology
    Volume116
    ISSN (Print)0074-7742

    Keywords

    • Behavior
    • Brain
    • Next-generation sequencing
    • RNA-seq
    • Transcriptome

    ASJC Scopus subject areas

    • Clinical Neurology
    • Cellular and Molecular Neuroscience

    Fingerprint

    Dive into the research topics of 'Introduction to sequencing the brain transcriptome'. Together they form a unique fingerprint.

    Cite this