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Transcriptome Studies in Trypanosoma cruzi Using RNA-seq

  • Gonzalo Greif
  • Luisa Berná
  • Florencia Díaz-Viraqué
  • Carlos RobelloEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1955)

Abstract

RNA-seq is a powerful method to study in detail transcriptome changes in defined conditions, providing enormous amount of information on RNA stability and gene regulation. In this chapter, we describe a directional and a nondirectional library preparation protocol for RNA-seq in Trypanosoma cruzi, as well as a pipeline for bioinformatic analysis, which includes read trimming, alignment to a reference genome, and differential expression.

Key words

Trypanosoma cruzi RNA-seq Gene expression Differential expression Bioinformatic pipeline 

Supplementary material

464546_1_En_3_MOESM1_ESM.pdf (228 kb)
Supplementary Material 1 Transcripts abundance quantification using Erange (PDF 228 kb)
464546_1_En_3_MOESM2_ESM.docx (15 kb)
Supplementary Material 2 DESeq pipeline (DOCX 14 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Gonzalo Greif
    • 1
  • Luisa Berná
    • 1
  • Florencia Díaz-Viraqué
    • 1
  • Carlos Robello
    • 1
    • 2
    Email author
  1. 1.Laboratory of Host Pathogen Interactions-UBMInstitut Pasteur de MontevideoMontevideoUruguay
  2. 2.Departamento de BioquímicaFacultad de Medicina-UDELARMontevideoUruguay

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