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) Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”

Organism:

Pyrococcus furiosus

Type:

Other

Platform:

GPL28793

2 Samples

Download data: TXT, 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; Methanocaldococcus jannaschii; Saccharolobus solfataricus; Pyrococcus furiosus

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:

GPL24874 GPL24873

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:

GPL22336 GPL22337

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) DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. more...

Organism:

Lactococcus lactis subsp. lactis; Lactiplantibacillus plantarum; Lachnobacterium bovis; Clostridium perfringens ATCC 13124; Methanocaldococcus jannaschii DSM 2661; Methylorubrum extorquens AM1; Thermoplasma volcanium GSS1; Acidobacteriaceae bacterium TAA 166; Mycoplasmopsis bovis PG45; Methanospirillum hungatei JF-1; Actinobacillus succinogenes 130Z; Fervidobacterium nodosum Rt17-B1; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Staphylothermus marinus F1; Thermoanaerobacter sp. X514; Xenorhabdus nematophila ATCC 19061; Galbibacter orientalis; Dyadobacter fermentans DSM 18053; Streptosporangium roseum DSM 43021; Pedobacter heparinus DSM 2366; Rhizobium etli CIAT 652; Meiothermus ruber DSM 1279; Planctopirus limnophila DSM 3776; Methanothermus fervidus DSM 2088; Sebaldella termitidis ATCC 33386; Methanohalophilus mahii DSM 5219; Aminobacterium colombiense DSM 12261; Acidobacteriaceae bacterium KBS 146; Pontibacter actiniarum DSM 19842; Thermobacillus composti KWC4; Marinithermus hydrothermalis DSM 14884; Bernardetia litoralis DSM 6794; Desulfobacca acetoxidans DSM 11109; Rikenella microfusus DSM 15922; Echinicola vietnamensis DSM 17526; Orenia marismortui DSM 5156; Sporocytophaga myxococcoides DSM 11118; Niabella soli DSM 19437; Sinorhizobium medicae WSM1115; Hippea alviniae EP5-r; Hippea sp. KM1; Sphingomonas melonis C3; Methylophilaceae bacterium 11; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Solidesulfovibrio cf. magneticus IFRC170; Desulfotignum balticum DSM 7044; Methylobacterium sp. EUR3 AL-11; Kallotenue papyrolyticum; Bryobacter aggregatus MPL3; Ruminococcus albus AD2013; Eubacterium sp. AB3007; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Selenomonas ruminantium AC2024; Selenomonas sp. AB3002; Peptostreptococcaceae bacterium VA2; Ruminococcus sp. HUN007; Teredinibacter turnerae; Escherichia coli CFT073; Salmonella bongori NCTC 12419; Treponema denticola ATCC 35405; Akkermansia muciniphila ATCC BAA-835; Phaeobacter inhibens DSM 17395; Actinosynnema mirum DSM 43827; Staphylococcus aureus subsp. aureus USA300_TCH1516; Sphaerobacter thermophilus DSM 20745; Veillonella parvula DSM 2008; Streptobacillus moniliformis DSM 12112; Allomeiothermus silvanus DSM 9946; Sedimentitalea nanhaiensis DSM 24252; Sediminispirochaeta smaragdinae DSM 11293; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Syntrophothermus lipocalidus DSM 12680; Stutzerimonas stutzeri RCH2; Syntrophobotulus glycolicus DSM 8271; Bacillus spizizenii str. W23; Phocaeicola salanitronis DSM 18170; Pseudofrankia sp. DC12; Nitratifractor salsuginis DSM 16511; Cellulophaga lytica DSM 7489; Asinibacterium sp. OR53; Solitalea canadensis DSM 3403; Patulibacter minatonensis DSM 18081; Acetobacterium woodii DSM 1030; Nocardia sp. BMG51109; Halomicrobium katesii DSM 19301; Nitriliruptor alkaliphilus DSM 45188; Methylophilus sp. 1; Pseudomonas aeruginosa NCAIM B.001380; Kangiella aquimarina DSM 16071; Pelobacter seleniigenes DSM 18267; Thiomicrospira pelophila DSM 1534; Desulfurobacterium sp. TC5-1; Bacteroides sp. 14(A); Clostridium sp. 12(A); Hydrogenovibrio kuenenii DSM 12350; Leptolyngbya sp. PCC 6406; Maribacter sp. Hel_I_7; Desulfospira joergensenii DSM 10085; Tolumonas lignilytica; Cellvibrionaceae bacterium 1162T.S.0a.05; Lacrimispora indolis SR3; Lacrimispora indolis DSM 755; Desulforegula conservatrix Mb1Pa; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfohalovibrio reitneri; Alicyclobacillus macrosporangiidus CPP55; Pseudacidobacterium ailaaui; Mediterraneibacter gnavus AGR2154; Sediminibacter sp. Hel_I_10; Hydrogenovibrio sp. MA2-6; Pseudobutyrivibrio ruminis HUN009; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210; Enterococcus gallinarum; Clostridium algidicarnis; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Agrobacterium fabrum str. C58; Persephonella; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Clostridioides difficile 630; Thiobacillus denitrificans ATCC 25259; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Sulfurimonas denitrificans DSM 1251; Sulfolobus acidocaldarius DSM 639; Flavobacterium psychrophilum JIP02/86; Methanocorpusculum labreanum Z; Cronobacter; Pseudarthrobacter chlorophenolicus A6; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Thermanaerovibrio acidaminovorans DSM 6589; Corynebacterium aurimucosum ATCC 700975; Zymomonas mobilis subsp. pomaceae ATCC 29192; Klebsiella aerogenes FGI35; Cellulophaga algicola DSM 14237; Flexistipes sinusarabici DSM 4947; Sulfurospirillum barnesii SES-3; Gillisia limnaea DSM 15749; Spirochaeta thermophila DSM 6578; Ruminococcus sp. NK3A76; Spirochaeta africana DSM 8902; Holophaga foetida DSM 6591; Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7; Acetivibrio clariflavus 4-2a; Thermacetogenium phaeum DSM 12270; Methylophilus sp. 5; Arthrobacter sp. 31Y; Methylophilus sp. 42; Methylotenera versatilis 79; Psychrilyobacter atlanticus DSM 19335; Prevotella sp. 10(H); Methylotenera sp. 73s; Acidovorax sp. JHL-3; Gillisia sp. JM1; Cellulomonas sp. KRMCY2; Clostridium sp. ASBs410; Limisalsivibrio acetivorans; Polaromonas sp. EUR3 1.2.1; Levilactobacillus brevis AG48; Pediococcus acidilactici AGR20; Exiguobacterium chiriqhucha; Prevotella sp. HUN102; Flavimarina sp. Hel_I_48; Lachnospiraceae bacterium AC2012; Clostridioides mangenotii LM2; Exiguobacterium aurantiacum DSM 6208; Exiguobacterium acetylicum DSM 20416; Exiguobacterium oxidotolerans JCM 12280; Exiguobacterium antarcticum DSM 14480; Methylobacter tundripaludum 21/22; Lachnoclostridium phytofermentans KNHs2132; Staphylococcus epidermidis AG42; Butyrivibrio sp. AE3003; Streptococcus equinus; Salmonella enterica subsp. arizonae serovar 62:z4,z23:-; Xylella fastidiosa Temecula1; Acetivibrio thermocellus ATCC 27405; Rhodopseudomonas palustris CGA009; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Hydrogenovibrio crunogenus XCL-2; Chloroflexus aggregans DSM 9485; Thermosipho melanesiensis BI429; Shewanella woodyi ATCC 51908; Bradyrhizobium elkanii USDA 76; Dinoroseobacter shibae DFL 12 = DSM 16493; Parabacteroides distasonis ATCC 8503; Anoxybacillus flavithermus WK1; Escherichia coli str. K-12 substr. MG1655; Capnocytophaga ochracea DSM 7271; Haloterrigena turkmenica DSM 5511; Palaeococcus ferrophilus DSM 13482; Acetivibrio thermocellus DSM 1313; Gracilinema caldarium DSM 7334; Treponema succinifaciens DSM 2489; Caldithrix abyssi DSM 13497; Calidithermus chliarophilus DSM 9957; Cohnella panacarvi Gsoil 349; Methylobacterium sp. 10; Xanthobacter sp. 91; Geopsychrobacter electrodiphilus DSM 16401; Hydrogenovibrio marinus DSM 11271; Nocardia sp. BMG111209; Klebsiella oxytoca BRL6-2; Polaribacter sp. Hel_I_88; Methylohalobius crimeensis 10Ki; Streptomyces sp. WMMB 714; Ruminiclostridium josui JCM 17888; Alteromonas sp. ALT199; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; Microbacterium sp. KROCY2; Thermogemmatispora carboxidivorans; Ruminococcus flavefaciens AE3010; Butyrivibrio sp. FCS014; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Butyrivibrio sp. AE3004; Teredinibacter purpureus

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(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) Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. more...

Organism:

Pyrococcus yayanosii; Pyrococcus furiosus; Pyrococcus

Type:

Expression profiling by array

Platform:

GPL20888

15 Samples

Download data: TXT