Introduction to sequencing the brain transcriptome

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

Research output: Contribution to journalArticle

9 Citations (Scopus)

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)
Pages (from-to)1-19
Number of pages19
JournalInternational Review of Neurobiology
Volume116
DOIs
StatePublished - 2014

Fingerprint

Transcriptome
RNA
Brain
Untranslated RNA
Gene Regulatory Networks
Brain Diseases
Substance-Related Disorders
Single Nucleotide Polymorphism
Exons
Schizophrenia
Genotype
Technology
Genes

Keywords

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

ASJC Scopus subject areas

  • Clinical Neurology
  • Cellular and Molecular Neuroscience

Cite this

Introduction to sequencing the brain transcriptome. / Hitzemann, Robert; Darakjian, Priscila; Walter, Nikki; Iancu, Ovidiu; Searles, Robert; McWeeney, Shannon.

In: International Review of Neurobiology, Vol. 116, 2014, p. 1-19.

Research output: Contribution to journalArticle

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