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Transcriptomics Using Next Generation Sequencing Technologies

  • Dasfne Lee-Liu
  • Leonardo I. Almonacid
  • Fernando Faunes
  • Francisco Melo
  • Juan Larrain
Part of the Methods in Molecular Biology book series (MIMB, volume 917)

Abstract

Next generation sequencing technologies may now be applied to the study of transcriptomics. RNA-Seq or RNA sequencing employs high-throughput sequencing of complementary DNA fragments delivering a transcriptional profile. In this chapter, we aim to provide a starting point for Xenopus researchers planning on starting an RNA-Seq transcriptomics study. We begin by providing a section on template isolation and library preparation. The next section comprises the main bioinformatics procedures that need to be performed for raw data processing, normalization, and differential gene expression. Finally, we have included a section on studying deep sequencing results in Xenopus, which offers general guidance as to what can be done in this model.

Key words

Xenopus tropicalis Xenopus laevis RNA-Seq Small RNA-Seq Transcriptomics Transcriptional profiling High-throughput sequencing Next generation sequencing Massively ­parallel sequencing Illumina 

Notes

Acknowledgements

This work was funded by research grants from FONDECYT (No. 1110400), ICM (No. P09-016-F) (LIA and FM), Center for Aging and Regeneration (CARE), and Millennium Nucleus in Regenerative Biology (MINREB) (DLL, FF, JL). We thank Dr. Mauricio Moreno for providing information on RNA yield from Xenopus embryos.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Dasfne Lee-Liu
    • 1
  • Leonardo I. Almonacid
    • 2
  • Fernando Faunes
    • 1
  • Francisco Melo
    • 3
  • Juan Larrain
    • 1
  1. 1.Center for Aging and Regeneration and Millennium Nucleus in Regenerative BiologyPontificia Universidad Catolica de ChileSantiagoChile
  2. 2.Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and ImmunotherapyPontificia Universidad Catolica de ChileSantiagoChile
  3. 3.Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and ImmunotheraphyPontificia Universidad Catolica de ChileSantiagoChile

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