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Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing
Pfreundt, U.; Miller, D.; Adusumilli, L.; Stambler, N.; Berman-Frank, I.; Hess, W.R. (2014). Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing. Marine Genomics 18(Part B): 93-95. https://dx.doi.org/10.1016/j.margen.2014.06.005
In: Marine Genomics. Elsevier: Amsterdam. ISSN 1874-7787; e-ISSN 1876-7478, meer
Peer reviewed article  
Beschikbaar in  Auteurs 
Trefwoorden
    Marine Sciences
    Marine Sciences > Marine Genomics
    Scientific Community
    Scientific Publication
    Marien/Kust
Author keywords
    Gene expression; Metatranscriptomics; Microbial community; RNA-Seq;Transcriptome
Project Top | Auteurs 
  • Association of European marine biological laboratories, meer
Auteurs  Top 
  • Pfreundt, U.
  • Miller, D.
  • Adusumilli, L.
  • Stambler, N.
  • Berman-Frank, I.
  • Hess, W.R.
Abstract
    Metatranscriptomics is a widely used approach to study the gene expression within a whole microbial community. Spatial or temporal differences observed between datasets point to transcriptional responses to changes or alterations in the community's environment. No transcriptomic data has yet been published from the oligotrophic Gulf of Aqaba/Eilat, northern Red Sea. The primary objective of this study was to create a depth-specific snapshot of community gene expression ranging from the surface waters to the bottom of the mixed-layer depth during winter when thermal destratification occurs. Our secondary objective was to compare two different methods for transcriptome analysis. While random RNA sequencing (RNA-seq) is routinely used, differential RNA sequencing (dRNA-seq, enriched in primary transcripts) has never been used for metatranscriptomics. In this dataset, we used dRNA-seq for samples that were collected from three depths while applying RNA-seq for one of the samples to obtain direct comparison between the methods. We de-novo assembled the reads into contigs and show a high percentage of reads mapping back to the contigs, supporting the validity of the assembly.
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