GEO DataSets

(Submitter supplied) Transcriptome of the wild type (WT) of S. melonis TY and snc137 deleted cells carrying either a plasmid overexpressing SNC137 (Δsnc137 comp.), or an empty control vector (Δsnc137)

Organism:

Sphingomonas melonis TY

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32630

9 Samples

Download data: TXT

(Submitter supplied) Drought and salinity are most ubiquitous environmental factors that causing hyperosmotic threats to Sphingomonas and impairs their efficiency of performing environmental functions. However, bacteria have developed various responses and regulation systems to coping with these abiotic challenges. Among which post-transcriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions could lead to induction of specific small RNA (sRNA) that participates in stress response regulation. more...

Organism:

Sphingomonas melonis TY

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32630

9 Samples

Download data: TXT

(Submitter supplied) To further elucidate the responsive patterns of S. melonis TY to hyperosmotic stress at transcriptional level, transcriptome sequencings were carried out on S. melonis TY cultured under three levels of salt stress (0%, 1%, 2%) for 10 or 30 minutes.

Organism:

Sphingomonas melonis TY

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32630

21 Samples

Download data: TXT

(Submitter supplied) Bacterium Sphingomonas glacialis AAP5 isolated from the alpine lake Gossenköllesee contains genes for anoxygenic phototrophy as well as proton-pumping xanthorhodopsin. Here we show that AAP5 expresses xanthorhodopsin when illuminated at temperatures below 16°C. In contrast bacteriochlorophyll-containing reaction centers are expressed between 4 and 22°C in the dark. Thus, cells grown at lower temperature under natural light-dark cycle produced both photosystems. more...

Organism:

Sphingomonas glacialis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31936

28 Samples

Download data: TXT

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

Organism:

Sphingomonas sp. AAP5

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28277

21 Samples

Download data: TXT

(Submitter supplied) Comparison of cells grown under carbon-limited and carbon-replete conditions.

Organism:

Sphingomonas sp. AAP5

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28277

12 Samples

Download data: TXT

(Submitter supplied) Comparison of cells grown for 4 and 8 days on agar plates with cells from liquid cultures after reaching their maximum optical density.

Organism:

Sphingomonas sp. AAP5

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28277

9 Samples

Download data: TXT

(Submitter supplied) Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources.

Organism:

Sphingomonas sp. ATCC 31555

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21628

3 Samples

Download data: FA, 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:

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) Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.

Organism:

Sphingomonas sp. A1

Type:

Expression profiling by array

Platform:

GPL18221

2 Samples

Download data: PAIR

(Submitter supplied) Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K.

Organism:

Sphingomonas sp. A1

Type:

Expression profiling by array

Platform:

GPL18221

2 Samples

Download data: PAIR

(Submitter supplied) This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to short-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 4h after growth on a rich medium. Survival was monitored by plating and transcriptomic response was determined by whole-genome microarray analysis. The data showed no major differences were obsrved in gene expression and the viability of the cells were not affected during short-term incubation time

Organism:

Sphingomonas sp. LH128

Type:

Expression profiling by array

Platform:

GPL15623

6 Samples

Download data: TXT

(Submitter supplied) This study examines genome-wide expression of the phenanthrene-degrading Sphingomonas sp. LH128 as a response to long-term starvation stress. For this purpose, the strain was subjected to complete nutrient starvation for 6 months after growth on a rich medium. Survival was monitored by plating, physiological response was examined by flow cytometry and FAME analysis, and this response was related to transcriptomic response as determined by whole-genome microarray analysis. more...

Organism:

Sphingomonas sp. LH128

Type:

Expression profiling by array

Platform:

GPL15623

6 Samples

Download data: TXT

(Submitter supplied) The survival, pollutant degradation activity and transcriptome response was monitored in Sphingomonas sp. LH128 inoculated into soil. Cultivable cell numbers were determined by plating, while phenanthrene degradation was monitored by HPLC. The genetic base for the adaptive strategy of LH128 in soil was investigated by using microarray consisting 7,200 gene-coding ORFs. During 4 hours of incubation, 510 genes were differentially expressed (317 increased and 193 reduced expression) while 610 genes were differentially expressed (318 increased and 292 reduced) after 10 days of incubation. more...

Organism:

Sphingomonas sp. LH128

Type:

Expression profiling by array

Platform:

GPL15623

9 Samples

Download data: TXT

(Submitter supplied) This study examines the transcriptomic response of biofilms of the PAH-degrading Sphingomonas sp. LH128 on solute stress when actively degrading and growing on the PAH compound. To address the effect of solute stress on bacterial physiology and transcriptomic response, NaCl was used as osmolyte. Both acute and chronic solute stress was invoked to assess differences in short-term and long-term responses.

Organism:

Sphingomonas sp. LH128

Type:

Expression profiling by array

Platform:

GPL15623

9 Samples

Download data: TXT

(Submitter supplied) We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. more...

Organism:

Rhodococcus jostii RHA1; Bordetella sp. IITR-02; Escherichia coli BL21; freshwater sediment metagenome; synthetic construct; Escherichia coli DH5[alpha]; Escherichia coli K-12; Sphingomonas sp. NM05; soil metagenome

Type:

Genome variation profiling by array

Platform:

GPL10926

17 Samples

Download data: TXT

(Submitter supplied) Studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. During the biodegradation kinetics with phenanthrene, fluoranthene or a mix of both pollutants, we identified the targeted set of genes induced by these pollutants, compared to basal expression detected with glucose. more...

Organism:

Sphingomonas paucimobilis; uncultured organism

Type:

Expression profiling by array

Platform:

GPL10343

17 Samples

Download data: PAIR

(Submitter supplied) In order to assess the effect on signal variability of the type of target used for oligonucleotide microarray experiments, we hybridized double and single stranded DNA of three genes on a Nimblegen High Density microarray. This slide carries specific probes (two lengths: 30 and 50 nucleotides, for a total of 7456 probes) targeting every region of selected genes.

Organism:

Sphingomonas paucimobilis; Dehalococcoides mccartyi VS; Methylosinus trichosporium OB3b; Methylosinus trichosporium

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL10729

6 Samples

Download data: PAIR