UNIT 4.11 RNA-Seq: A Method for Comprehensive Transcriptome Analysis

  1. Ugrappa Nagalakshmi,
  2. Karl Waern,
  3. Michael Snyder

Published Online: 1 JAN 2010

DOI: 10.1002/0471142727.mb0411s89

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Nagalakshmi, U., Waern, K. and Snyder, M. 2010. RNA-Seq: A Method for Comprehensive Transcriptome Analysis. Current Protocols in Molecular Biology. 89:II:4.11:4.11.1–4.11.13.

Author Information

  1. Molecular, Cellular, and Developmental Biology Department, Yale University, New Haven, Connecticut

Publication History

  1. Published Online: 1 JAN 2010
  2. Published Print: JAN 2010


A recently developed technique called RNA Sequencing (RNA-Seq) uses massively parallel sequencing to allow transcriptome analyses of genomes at a far higher resolution than is available with Sanger sequencing- and microarray-based methods. In the RNA-Seq method, complementary DNAs (cDNAs) generated from the RNA of interest are directly sequenced using next-generation sequencing technologies. The reads obtained from this can then be aligned to a reference genome in order to construct a whole-genome transcriptome map. RNA-Seq has been used successfully to precisely quantify transcript levels, confirm or revise previously annotated 5′ and 3′ ends of genes, and map exon/intron boundaries. This unit describes protocols for performing RNA-Seq using the Illumina sequencing platform. Curr. Protoc. Mol. Biol. 89:4.11.1-4.11.13. © 2010 by John Wiley & Sons, Inc.


  • RNA-Seq;
  • transcriptome;
  • high-throughput sequencing;
  • gene expression;
  • annotation;
  • cDNA library preparation