GEO DataSets

(Submitter supplied) We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. more...

Organism:

aquifer metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27730

29 Samples

Download data: BIOM, TXT

(Submitter supplied) 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.

Organism:

aquifer metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25546

8 Samples

Download data: HDF5, TXT

(Submitter supplied) Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. more...

Organism:

aquifer metagenome

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26069

15 Samples

Download data: FASTA

(Submitter supplied) The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the application of amplicon pyrosequencing. The possibility of barcode-tagged sequencing of templates gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing and, as in the early days of genetic community fingerprinting, pros and cons are continuously provided. more...

Organism:

Aliivibrio fischeri; environmental samples; environmental samples; environmental samples; aquifer metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL15200 GPL26069 GPL15201

21 Samples

Download data: FASTA, TXT