GEO DataSets

(Submitter supplied) RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. more...

Organism:

Thermococcus barophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33349

9 Samples

Download data: CSV, TXT

(Submitter supplied) In ordet to understand in vivo role of uncharacterized DNA-binding protein (TON_1525) in T. onnurineus NA1, TON_1525 gene deletion mutant was constructed. Also transcriptome analysis was perfomed between wild type and mutant strains to measure changed expression profile of genes by deletion of TON_1525 gene under CO supplemented medium.

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: XLSX

(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

(Submitter supplied) In this study, we generated allelic knockouts of ATP-dependent RNA ligase (Rnl) in hyperthermophilic archaeon T. kodakarensis and analyze the small RNAs.

Organism:

Thermococcus kodakarensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32423

4 Samples

Download data: XLSX

(Submitter supplied) In this study, we generated allelic knockouts of ATP-dependent RNA ligase (Rnl) in hyperthermophilic archaeon T. kodakarensis and analyze the total and small RNA by RNA-Seq.

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30910

4 Samples

Download data: TXT

(Submitter supplied) We used RNA-seq to determine expression of Thermococcus kodakarensis genes expressed from fosmids in E. coli

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27055

1 Sample

Download data: TXT

(Submitter supplied) Using the model organism Thermococcus kodakarensis, we genetically alter the chromatin landscape and quantify the resultant changes in gene expression, including unanticipated and significant impacts on provirus transcription. Global transcriptome changes resultant from varying chromatin landscapes reveal the regulatory importance of higher-order histone-based chromatin architectures in regulating gene expression.

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27055 GPL28639

10 Samples

Download data

(Submitter supplied) Hyperthermophilic archeaon, Thermococcus onnurineus NA1 has known as a strict anaerobe. To date, a few of studies have been reported that strict anaerobe can grow using oxygen. However, the research of the growth enhancement of strict anaerobic archaeon belonging to the order of Thermococcales using the oxygen, in which has never been reported so far. In this study, we showed that the growth of T. onnurineus NA1 strain increased under various oxygen concentrations and we observed that oxygen was decreased in the headspace during the growth of cell. more...

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: XLSX

(Submitter supplied) N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification, present on tRNA, rRNA and recently investigated in eukaryotic mRNA. We report ac4C-seq, a chemical genomic method for single-nucleotide resolution, transcriptome-wide quantitative mapping of ac4C. While we did not find detectable ac4C sites in human and yeast mRNAs, ac4C was induced via ectopic overexpression of eukaryotic acetyltransferase complexes, invariably at a conserved sequence motif. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens; Thermococcus sp. AM4; Thermococcus kodakarensis; Pyrococcus furiosus; Methanocaldococcus jannaschii; Saccharolobus solfataricus

Type:

Other

8 related Platforms

96 Samples

Download data: XLSX

(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:

Thermococcus paralvinellae; Methanocaldococcus jannaschii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24873 GPL24874

13 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) 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 present study describes the isolation of a Thermococcus sp. strain 175 from the world‘s deepest hydrothermal vent sites known thus far – The Mid-Cayman Rise.consisting of two hydrothermal venting systems Bee Bee (or Piccard), at 4950m depth and Von Damm (or Walsh) at 2300m The strain is capable of growth over 0.1MPa (atm. Pressure) to 120MPa, the widest known range of pressure dependent growth. The study further explores piezophilic adaptation using comparative genomic tools. Insights into the transcriptome of this strain providers the first look into the transcriptional machinery of peizophilic Thermococci.

Organism:

Thermococcus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20620

6 Samples

Download data: FNA, XLSX

(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:

GPL22337 GPL22336

7 Samples

Download data: TXT

(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) A hyperthermophilic archaeon Thermococcus kodakarensis can grow in a wide range of temperatures from 60°C to 93°C, optimally at 85°C. To screen the genes that being specifically expressed at lowest growth temperature, 60°C, we investigated the transcriptional profilings of T. kodakarensis grown at 60˚C by comparing with those grown at 85°C.

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by array

Platform:

GPL17565

2 Samples

Download data: TXT

(Submitter supplied) Thermococcus kodakarensis preferentially utilizes amino acids as carbon and energy sources in the presence of elemental sulfur as a terminal electron acceptor, while it can assimilate and grow on starch or pyruvate using proton as a terminal acceptor, generating hydrogen in the absence of elemental sulfur. SurR is a transcriptional regulator controlling hydrogen and elemental sulfur metabolism. To identify the genes that are under the regulation of Tk-SurR, we investigated the transcriptional profiling of Tk-SurR deletion strain grown in the presence of elemental sulfur at 85˚C by comparing with the host strain, KU216.

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by array

Platform:

GPL17565

2 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) Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts. To date, such studies have investigated primarily Bacteria. more...

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18473

5 Samples

Download data: WIG

(Submitter supplied) Thermococcus kodakarensis, which can grow in a wide range of temperatures, from 60°C to 100°C, optimally at 85°C, has two transcription factor Bs, TFB1 and TFB2, both of which are basal transcription factor. TFB1 is unique to hyperthermophiles, but TFB2 is widely conserved in Euryarchaeota. To screen the genes dependent on each TFB in a temperature dependent manner, we investigated the transcriptional profilings of each TFB deletant strain grown at each temperature, 60˚C, 85˚C, and 93˚C, by comparing with the host strain, KU216. more...

Organism:

Thermococcus kodakarensis

Type:

Expression profiling by array

Platform:

GPL17565

12 Samples

Download data: TXT