title: Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing.
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.
authors.affiliation: Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Pfreundt
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Dan
authors.initials: D
authors.lastname: Miller
authors.affiliation: Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Adusumilli
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Noga
authors.initials: N
authors.lastname: Stambler
authors.affiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
authors.forename: Ilana
authors.initials: I
authors.lastname: Berman-Frank
authors.affiliation: Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany. Electronic address: wolfgang.hess@biologie.uni-freiburg.de.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D019156:Indian Ocean; D054892:Metagenome / Q000235:genetics*; D008969:Molecular Sequence Data; D010933:Plankton / Q000235:genetics*; D012621:Seasons; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*; D014872:Water Movements
chemical_list: D017931:DNA Primers
keywords: Gene expression; Metatranscriptomics; Microbial community; RNA-Seq; Transcriptome