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Series GSE119644 Query DataSets for GSE119644
Status Public on Sep 07, 2018
Title Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into hypoxic pollutant-degrading aquifer microbiota
Organism aquifer metagenome
Experiment type Expression profiling by high throughput sequencing
Other
Summary We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.
 
Overall design Microcosms were made using sediment from a hypoxic, hydrocarbon-contaminated aquifer in Siklos, Hungary. They were incubated under hypoxic/microoxic conditions and provided with isotopically-labeled toluene as a substrate. RNA was extracted and subjected to isopycnic centrifugation to separated heavy (isotopically labeled) and light (unlabeled) RNA, representing microbes which did or did not metabolize toluene, respectively. Total RNA was sequenced to provide both taxonimic (16S) and functional (mRNA) data on this microbiota, the first instance of total-RNA-stable isotope probing used to investigate a contaminated environment.
 
Contributor(s) Bradford LM, Lueders T
Citation(s) 30483229
Submission date Sep 07, 2018
Last update date Dec 06, 2018
Contact name Tillmann Lueders
E-mail(s) tillmann.lueders@uni-bayreuth.de
Phone 49921555640
Organization name Universitaet Bayreuth
Department Lehrstuhl Ökologische Mikrobiologie (ÖMIK)
Street address Dr.-Hans-Frisch-Straße 1-3
City Bayreuth
State/province Bayern
ZIP/Postal code 95448
Country Germany
 
Platforms (1)
GPL25546 Illumina NextSeq 500 (aquifer metagenome)
Samples (8)
GSM3380030 12CHunamp
GSM3380031 12CLunamp
GSM3380032 13CHunamp
Relations
BioProject PRJNA489848
SRA SRP160141

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119644_KEGG_functional.txt.gz 55.0 Kb (ftp)(http) TXT
GSE119644_KEGG_relative.megan.txt.gz 64.8 Kb (ftp)(http) TXT
GSE119644_otu_table_filtered.biom.HDF5 447.8 Kb (ftp)(http) HDF5
GSE119644_otu_table_filtered.txt.gz 32.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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