GEO DataSets

(Submitter supplied) A Type II VapB14 Antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius, not only through traditional Toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC Toxins are ribonucleases that are neutralized by their proteinaceous cognate Type II VapB Antitoxin. VapB Antitoxins have a flexible tail at their C-terminus that covers the Toxin’s active site neutralizing its activity. more...

Organism:

Sulfolobus acidocaldarius; Sulfolobus acidocaldarius DSM 639

Type:

Expression profiling by array

Platform:

GPL33204

4 Samples

Download data: GPR, TXT

(Submitter supplied) Chromosome conformation capture (3C) technologies have identified topologically associating domains (TADs) and larger A/B compartments as two salient structural features of eukaryotic chromosomes. These structures are sculpted by the combined actions of transcription and structural maintenance of chromosomes (SMC) superfamily proteins. Bacterial chromosomes fold into TAD-like chromosomal interaction domains (CIDs) but do not display A/B compartment-type organization. more...

Organism:

Sulfolobus islandicus; Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL26274 GPL26275

31 Samples

Download data: TXT

(Submitter supplied) Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. more...

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24283

2 Samples

Download data: TXT

(Submitter supplied) Extremophilic archaea like all organisms experience potentially life-threatening conditions including UV light, which induces severe DNA damage. Since the alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, we investigated the expression of TFB3 on protein level including in vivo protein-protein interaction studies, tfb3 reporter gene assays and creation of a tfb3 insertion mutant to study early differential gene expression upon UV treatment (after 45 and 90 minutes). more...

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24749

18 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26274

12 Samples

Download data: TXT

(Submitter supplied) We report the regulon of a GntR-like regulator from the archaeon Sulfolobus acidocaldarius by looking at differentially expressed genes comparing a YtrASa overexpression strain with its isogenic wild ype

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26274

6 Samples

Download data: TXT

(Submitter supplied) We report the characterization of GntR-like regulator in the Archaeon Sulfolobus acidocaldarius by looking at the genome wide interaction map of the protein in vivo

Organism:

Sulfolobus acidocaldarius

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26274

6 Samples

Download data: TXT

(Submitter supplied) The three-dimensional organization of chromosomes can have a profound impact on their replication and expression. The chromosomes of higher eukaryotes possess discrete compartments that are characterized by differing transcriptional activities. Contrastingly, most bacterial chromosomes have simpler organization with local domains, the boundaries of which are influenced by gene expression. Numerous studies have revealed that the higher-order architectures of bacterial and eukaryotic chromosomes are dependent on the actions of Structural Maintenance of Chromosomes (SMC) superfamily protein complexes, in particular the near-universal condensin complex. more...

Organism:

Sulfolobus acidocaldarius; Sulfolobus islandicus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

94 Samples

Download data: TXT

(Submitter supplied) This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. more...

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24749 GPL24939

18 Samples

Download data: TXT

(Submitter supplied) This is ChIPseq result of FadR (Saci_1107), which is the only TetR family regulator presented in Sulfolobus acidocaldarius. The aim of the study is to gain insights into the function of TetR regulator by analyzing its whole genome binding sites.

Organism:

Sulfolobus acidocaldarius DSM 639

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24388

6 Samples

Download data: BEDGRAPH

(Submitter supplied) To unravel the regulon of FadR (Saci_1107), comparative transcriptomic analysis was performed for the fadR deletion mutant versus the isogenic WT strain using RNA-seq approach.

Organism:

Sulfolobus acidocaldarius DSM 639

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24383

4 Samples

Download data: CSV, TXT

(Submitter supplied) Total RNAs were isolated from the thermophilic archaeon Sulfolobus acidocaldarius MW001 and subjected to Illumina sequencing. A differential gene expression analysis was performed to identify ncRNA in biofilm- associated cells and planktonically grown cells. Additionally, the small RNA subpopulation of the transcriptome was subjected to RNaseR digestion prior to Illumina sequencing. An abundant double-stranded RNA was identified. more...

Organism:

Sulfolobus acidocaldarius

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23051

3 Samples

Download data: TXT, WIG

(Submitter supplied) Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. more...

Organism:

Sulfolobus acidocaldarius

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23051 GPL23429

5 Samples

Download data: WIG

(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:

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; 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; 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; 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

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(Submitter supplied) Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. more...

Organism:

Sulfolobus acidocaldarius DSM 639

Type:

Expression profiling by array

Platform:

GPL10391

9 Samples

Download data: PAIR

(Submitter supplied) Spotted whole-genome 60-mer oligonucleotide microarray slides were used, based on 2278 protein-coding open reading frames (ORFs) from the S. acidocaldarius DSM 639 genome. Spots were printed in five replicates onto SuperChip aminopropylsilane coated slides (ThermoFisher) using a Qarray Mini microarray printer (Genetix) and UV crosslinked (600?mJ)

Organism:

Sulfolobus acidocaldarius DSM 639

1 Series

4 Samples

Download data