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SRX8709480: Shotgun metatranscriptome sequences of water column RNA: river water sample
1 ILLUMINA (Illumina HiSeq 4000) run: 2.8M spots, 833.5M bases, 341.4Mb downloads

Design: RNA-seq library was constructed after rRNA depletion using Ribo-Zero (Bacterial) Removal Kit (Illumina, Inc.). rRNA-depleted RNA was reverse-transcribed using SuperScript III First-Strand Synthesis System (ThermoFischer Scientific), converted to double-strand cDNA using NEBNext mRNA Second Strand Synthesis Module (New England Biolabs, Ipswich, MA), and subjected to Nextera XT DNA Library Preparation Kit (Illumina) for paired-end (2 x 150) sequencing on a HiSeq4000 sequencer (Illumina Inc., San Diego, CA) at the University of Oregon Genomics & Cell Characterization Core Facility (GC3F). The archived fastq sequence file includes sequences concatenated from several sequencing runs.
Submitted by: Oregon State University
Study: ROMEO: Metagenomic and Metatranscriptomic response of riverine microbial communities to seasonal changes in the composition of dissolved organic matter.
show Abstracthide Abstract
Rivers are the principle conduits between the major global organic carbon stores on land and those in the ocean. Dissolved organic matter (DOM) is a master variable in rivers, impacting light attenuation, metal transport, and metabolism. Riverine bacteria rely on DOM for sustenance and, in using DOM, respire a fraction and alter the composition of the remaining DOM. The relationship between microbes and DOM is a crucial but poorly understood shaper of river ecosystem function. One major gap is our understanding of specific metabolic capabilities of bacteria and how they interact with organic matter quality to carry out the key ecosystem function of transforming and metabolizing riverborne DOM. The ROMEO project (River Organic Matter and Environmental 'Omics) integrates new and cutting-edge tools in genetics and DOM geochemistry to describe in molecular detail the ecological and genetic mechanisms by which terrestrial DOM is modified and mineralized to carbon dioxide during transport from land to sea by determining the interactions and feedbacks between microbial functional diversity, gene expression, and DOM metabolism in U.S. rivers.
Sample: ROMEO2015.028.RNA_2015-09-21_Yuk_A_summer_river_water
SAMN15506178 • SRS6986061 • All experiments • All runs
Library:
Name: ROMEO2015.028.RNA.GC3F823_873_909_1270
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: METATRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 2.8M spots, 833.5M bases, 341.4Mb
Run# of Spots# of BasesSizePublished
SRR121972942,759,833833.5M341.4Mb2021-07-01

ID:
11332068

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