Pfreundt Ulrike, Miller Dan, Adusumilli Lakshmi, Stambler Noga, Berman-Frank Ilana, Hess Wolfgang R
Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
Mar Genomics. 2014 Dec;18 Pt B:93-5. doi: 10.1016/j.margen.2014.06.005. Epub 2014 Jun 28.
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.
宏转录组学是一种广泛应用于研究整个微生物群落内基因表达的方法。数据集中观察到的空间或时间差异表明了对群落环境变化的转录反应。红海北部贫营养的亚喀巴湾/埃拉特湾尚未发表过转录组学数据。本研究的主要目的是创建一个特定深度的群落基因表达快照，涵盖冬季热分层消失时从表层水到混合层深度底部的范围。我们的次要目的是比较两种不同的转录组分析方法。虽然随机RNA测序（RNA-seq）是常规使用的方法，但差异RNA测序（dRNA-seq，富集初级转录本）从未用于宏转录组学。在这个数据集中，我们对从三个深度采集的样本使用dRNA-seq，同时对其中一个样本应用RNA-seq，以获得两种方法之间的直接比较。我们将读数进行从头组装成重叠群，并显示出高比例的读数映射回重叠群，支持了组装的有效性。
