Transcriptome analysis using RNA-Seq

Wieteke A.M. Hoeijmakers, Richárd Bártfai, Hendrik G. Stunnenberg

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

33 Citations (Scopus)

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 m g 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.

Original languageEnglish
Title of host publicationMalaria
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages221-239
Number of pages19
ISBN (Print)9781627030250
DOIs
Publication statusPublished - 2013
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume923
ISSN (Print)1064-3745

Keywords

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

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