martes, 7 de mayo de 2019

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions | BMC Research Notes | Full Text

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions | BMC Research Notes | Full Text

BMC Research Notes

Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions

BMC Research Notes201912:250
  • Received: 19 March 2019
  • Accepted: 25 April 2019
  • Published: 

Abstract

Objective

The objective of this experiment was to identify transcripts in baker’s yeast (Saccharomyces cerevisiae) that could have originated from previously non-coding genomic regions, or de novo. We generated this data to be able to compare the transcriptomes of different species of Ascomycota.

Data description

We generated high-depth RNA sequencing data for 11 species of yeast: Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces kudriavzevii, Saccharomyces bayanus, Naumovia castelii, Kluyveromycelactis, Lachancea waltii, Lachancea thermotolerans, Lachancea kluyveri, and Schizosaccharomyces pombe. Using RNA-Seq from yeast grown in rich and oxidative conditions we created genome-guided de novo assemblies of the transcriptomes for each species. We included synthetic spike-in transcripts in each sample to determine the lower limit of detection of the sequencing platform as well as the reliability of our de novo transcriptome assembly pipeline. We subsequently compared the de novo transcripts assemblies to the reference gene annotations and generated assemblies that comprised both annotated and novel transcripts.

Keywords

  • RNA-seq
  • Yeast
  • Transcriptomics
  • De novo transcript assembly
  • De novo gene
  • Gene annotation

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