GEO DataSets

(Submitter supplied) Purpose: Compare the transcriptomes of T. paralvinellae using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown on different carbon sources, under optimal and hydrogen stress conditions. Methods: T. paralvinellae was grown in triplicate at with either 0.5% maltose or 0.5% tryptone to investigate its catabolic pathways when grown on a sugar and peptides, respectively. more...

Organism:

Thermococcus paralvinellae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23684

15 Samples

Download data: TXT

(Submitter supplied) The purpose of this experiment was to compare the transcriptomes of M. jannaschii using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown under H2-replete, H2-limited and H2-syntrophy conditions. The RNA-seq reads were mapped to both M. jannaschii and T. paralvinellae genomes using BBSplit from BBMap package. BBSplit is an aligner tool that bins sequencing reads by mapping to them multiple references simultaneously and separates the reads that map to multiple references to a special "ambiguous" file for each of them. more...

Organism:

Methanocaldococcus jannaschii; Thermococcus paralvinellae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24873 GPL24874

13 Samples

Download data: TXT

(Submitter supplied) A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H2 by carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. more...

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in an Frh-deficient mutant, Frh overexpression mutant and TON_0282 deletion mutant, compared to the wild-type strain. In this study, as a first step to assess the role of the frhAGB-encoding hydrogenases and TON_0282 gene, we constructed three mutants by deleting each gene in a T. onnurineus NA1.

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by array

Platform:

GPL22562

8 Samples

Download data: CALLS, PAIR

(Submitter supplied) A hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on a variety of CO-containing feed stocks such as by-product gas generated from steel-mill process. In this study we applied a long-term adaptive evolution to enhance H2 productivity. Through serial transfer of cell cultures with carbon monoxide (CO) as an energy source, we observed physiological changes in cell density, CO consumption rate and H2 production rate. more...

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

7 Samples

Download data: TXT

(Submitter supplied) Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. more...

Organism:

Methanococcus maripaludis S2

Type:

Expression profiling by genome tiling array

Platform:

GPL15063

8 Samples

Download data: TXT

(Submitter supplied) Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. more...

Organism:

Thermococcus gammatolerans

Type:

Expression profiling by array

Platform:

GPL6958

24 Samples

Download data: GPR

(Submitter supplied) We show the transcriptomic landscape of the H2-producing archaeon Thermococcus onnurineus NA1 in response to different growth conditions using primary and whole transcriptome sequencing. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA boxes, A-rich B recognition elements (BREs), and promoter proximal element (PPE) motifs in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). more...

Organism:

Thermococcus onnurineus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22336 GPL22337

7 Samples

Download data: TXT

(Submitter supplied) Previously, we reported that the TON_1525 (T55I) (designated as MC11) strain showed superior activity in CO oxidation than the wild-type strain. To understand the in vivo role of TON_1525 in this strain on CO-supplemented medium, transcriptome changes were investigated.

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

6 Samples

Download data: XLSX