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

Mostra el registre complet Registre parcial de l'ítem

  • dc.contributor.author Blevins, William Robert, 1987-
  • dc.contributor.author Carey, Lucas, 1980-
  • dc.contributor.author Albà Soler, Mar
  • dc.date.accessioned 2019-06-05T08:24:13Z
  • dc.date.available 2019-06-05T08:24:13Z
  • dc.date.issued 2019
  • dc.description.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, Kluyveromyces lactis, 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.
  • dc.description.sponsorship The work was funded by the following grants: (1) BFU2015-65235-P Ministerio de Economía e Innovación (Spanish Government)-FEDER (EU). (2) BFU2015-68351-P Ministerio de Economía e Innovación (Spanish Government)-FEDER (EU). (3) MDM-2014-0370 “Maria de Maeztu” Programme for Units of Excellence in R&D (Spanish Government). (4) 2017SGR1054 Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya. (5) 2017SGR01020 Agència de Gestió d’Ajuts Universitaris i de Recerca Generalitat de Catalunya. (6) Predoctoral fellowship (FI, Generalitat de Catalunya) to WRB. Grants 1, 3 and 4 were used to cover lab expenses and to obtain the RNA samples from yeast cultures. Grants 2 and 5 were used for RNA sequencing. Grant 6 covered the salary of WRB. These funding bodies had no role in the design of the study, collection of the data, analysis of the results, or writing of the manuscript.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Blevins WR, Carey LB, Albà MM. Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions. BMC Res Notes. 2019;12(1):250. DOI: 10.1186/s13104-019-4286-0
  • dc.identifier.doi http://dx.doi.org/10.1186/s13104-019-4286-0
  • dc.identifier.issn 1756-0500
  • dc.identifier.uri http://hdl.handle.net/10230/41705
  • dc.language.iso eng
  • dc.publisher BioMed Central
  • dc.relation.ispartof BMC Research Notes. 2019;12(1):250
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-68351-P
  • dc.rights © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword RNA-seq
  • dc.subject.keyword Yeast
  • dc.subject.keyword Transcriptomics
  • dc.subject.keyword De novo transcript assembly
  • dc.subject.keyword De novo gene
  • dc.subject.keyword Gene annotation
  • dc.title Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

Col·leccions

Articles (Departament de Medicina i Ciències de la Vida)
Articles (Hospital del Mar Research Institute)