GEO DataSets

(Submitter supplied) In submerged cultivation of filamentous microbes, including actinomycetes, complex morphology is one of the critical process features for secondary metabolites production. Ansamitocin P-3 (AP-3), an antitumor agent, is a secondary metabolite produced by Actinosynnema pretiosum ATCC 31280. An excessive mycelial fragmentation of A. pretiosum ATCC 31280 was observed during the early stage of fermentation. more...

Organism:

Actinosynnema pretiosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25168

3 Samples

Download data: TXT

(Submitter supplied) In search of AP-3 resistant genes, ATCC 31280△ansaA (inactivation of ansamitocin pksA, in avoiding of the interruption of endogenous generated AP-3) were cultured under the addition of 0, 50, 100 and 200 mg/L exogenous AP-3 for 24 h and collected, for strains under 200 mg/L AP-3, samples after 48 h and 72 h were also collected, and the RNA samples were collected and sent for sequencing.

Organism:

Actinosynnema pretiosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25168

6 Samples

Download data: TXT

(Submitter supplied) To explore gene expression and search for the ansamitocin resistant genes during fermentation, total RNA of the ansmitocin high producer NXJ-24 and the wildtype strain ATCC31280 were extracted and sequenced. The gene expression values from day 1 to day 5 of NXJ-24 and day 5 of ATCC31280 were compared. 6 genes were considered most likely to be the ansamitocin transporter genes.

Organism:

Actinosynnema pretiosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25168

5 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:

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; 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

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(Submitter supplied) This series of microarry is the study of the transcriptional profile asm gene clusster of high Ansamitocin P3 producing mutants derived from isolating rifampicin resistant mutants. Background The Actinomycete Actinosynnema pretiosum ssp. auranticum has commercial importance due to its production of ansamitocin P-3 (AP-3), a potent antitumor agent. One method to improve the productivity of A. pretiosum is to genetically alter the regulation of ansamitocin biosynthesis by manipulating selected genes. more...

Organism:

Actinosynnema pretiosum

Type:

Expression profiling by array

Platform:

GPL7284

24 Samples

Download data: TXT

(Submitter supplied) 1.PCR products were obtained from PCR reactions on genomic DNA of A. pretiosum. The primers were designed based on DNA sequences, AF453501 and U33059 as discussed in Yu et. al., 2002, PNAS, 99:7968. The DNA were arrayed in Abgene 384-well plates. Each well contains 100-150 ng/ul of DNA. 2. Rearray 10 µL into 384-well, Abgene 384-well microarray plates (AB-1056/w). 3. Print arrays using Biorad chipwriter pro, after print run is completed, let slides dry through passive evaporation in the arrayer.

Organism:

Actinosynnema pretiosum

1 Series

24 Samples

Download data: TXT