Malaria pp 221-239

Part of the Methods in Molecular Biology book series (MIMB, volume 923) | Cite as

Transcriptome Analysis Using RNA-Seq

  • Wieteke A. M. Hoeijmakers
  • Richárd Bártfai
  • Hendrik G. Stunnenberg
Protocol

Abstract

Transcriptome analysis by next-generation sequencing (RNA-seq) allows investigation of a transcriptome at unsurpassed resolution. One major benefit is that RNA-seq is independent of a priori knowledge on the sequence under investigation, thereby also allowing analysis of poorly characterized Plasmodium species. Here we provide a detailed protocol for RNA isolation and fragmentation, ribosomal RNA depletion, and cDNA synthesis that enables the preparation of a sequencing library from 1 to 2 μg of total RNA. Although we focus our discussion on the quantitative measurement of gene expression, this protocol is suited for many applications of RNA-seq and allows analysis of most RNA species.

Key words

Plasmodium Plasmodium falciparum Transcriptome RNA-sequencing (RNA-seq) Next-generation sequencing (NGS) Linear amplification for deep sequencing (LADS) 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Wieteke A. M. Hoeijmakers
    • 1
  • Richárd Bártfai
    • 1
  • Hendrik G. Stunnenberg
    • 1
  1. 1.Department of Molecular BiologyNijmegen Center for Molecular Life SciencesNijmegenThe Netherlands

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