GEO DataSets

(Submitter supplied) Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and recalcitrant to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. more...

Organism:

Acinetobacter baumannii A118; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34012 GPL29525

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Respiration deficient S. aureus small colony variants (SCVs) frequently cause persistent infections, which necessitates they acquire iron, yet how SCVs obtain iron remains unknown. To address this, we created a stable hemB mutant in S. aureus USA300 strain LAC. The hemB SCV utilized exogenously supplied heme but was attenuated for growth under conditions of iron starvation. RNA-seq showed that both WT S. more...

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30628

15 Samples

Download data: XLSX

(Submitter supplied) Using improved and robust biochemical methods, we present the first global analysis of RNA-binding proteins (RBPs) and RNA-binding domains (RBDs) in clinically relevant and multi-drug resistant Gram-positive bacteria. To validate our results in silico, we developed novel bioinformatics tools that compare RBDome data with ligand-binding site predictions generated by five different algorithms on a large number of S. more...

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Other

Platforms:

GPL29525 GPL29526

12 Samples

Download data: BEDGRAPH, FA, GTF, TXT

(Submitter supplied) ArlRS is a two-component regulatory system in Staphylococcus aureus. Here we use RNA-sequencing to compare gene expression in a wild-type USA300 strain and an isogenic arlRS mutant.

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26637

6 Samples

Download data: CSV

(Submitter supplied) MgrA is a global regulator of gene expression in Staphylococcus aureus. Here we use RNA-sequencing to compare gene expression in a wild-type USA300 strain and an isogenic mgrA mutant.

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17544

6 Samples

Download data: CSV

(Submitter supplied) The fungal metabolite apicidin acts as a quorum sensing inhibitor in Staphylococcus aureus. Here we use RNA-sequencing to examine the effect of apicidin on gene expression, comparing to untreated wild-type and an agr quorum sensing mutant.

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17544

9 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus is an important human pathogen causing skin infection and many serious diseases such as pneumonia, sepsis, and toxic shock syndrome. In the bacterium, the membrane-bound protease FtsH plays important roles in the bacterial resistance to various stresses. This study was initiated to explain the strain-specific aggregation of the ftsH-deletion mutant of the Newman strain. To understand the molecular basis of the phenotype, we identified FtsH substrate proteins by comparing the protein contents of two different strains, Newman and USA300, and found that, in the strain Newman, a single nucleotide change in the sensor histidine kinase saeS gene placed the SaeRS two-component system under the control of FtsH, leading to the strain-specific cell-aggregation phenotype. more...

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22665

6 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is a worldwide pathogen that colonizes the human nasal cavity and is a major cause of respiratory and cutaneous infections. In the nasal cavity, S. aureus thrives with high concentrations of nitric oxide (NO) produced by the innate immune effectors and has available for growth slow metabolizing free hexoses, such as galactose. Here, we have used deep sequencing transcriptomic analysis (RNA-Seq) and 1H-NMR to uncover how S. more...

Organism:

Staphylococcus aureus subsp. aureus USA300_FPR3757

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23534

4 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is an important cause of human skin and soft tissue infections (SSTIs) globally. Notably, 80% of all SSTIs are caused by S. aureus, of which ~63% are abscesses and/or cellulitis. Although progress has been made, our knowledge of the host and pathogen factors that contribute to the pathogenesis of SSTIs is incomplete. To provide a more comprehensive view of this process, we monitored changes in the S. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL8069

7 Samples

Download data: CEL, CHP

(Submitter supplied) Drug discovery for novel anti-infectives is essential to meet the global health threat of antibiotic resistant bacterial infections, including those caused by Staphylococcus aureus1,2. Because ~90% of S. aureus infections involve skin and soft tissues (SSTIs)3,4, we hypothesized that developing anti-virulence therapeutics5,6 for SSTIs could minimize pressure on resistance development while sparing conventional antibiotics for control of systemic infections. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL8069

12 Samples

Download data: CEL, CHP

(Submitter supplied) Methicillin-resistant Staphylococcus aureus (MRSA) is the causative agent of serious hospital- and community-associated infections. Due to the global rise in community-associated MRSA, the respective lineages are increasingly introduced into hospitals. This raises the question whether and, if so, how they adapt to this new environment. The present study was aimed at investigating how MRSA isolates of the USA300 lineage, infamous for causing infections in the general population, have adapted to the hospital environment. more...

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17544

48 Samples

Download data: XLSX

(Submitter supplied) The translation inhibitor Linezolid is an important antibiotic of last resort against multiresistant gram-positive pathogens including MRSA. Linezolid is reported to specifically inhibit extracellular virulence factors, but the molecular cause is unknown. To elucidate the physiological response of S. aureus to Linezolid in general and the possible inhibition of virulence factors specifically we performed a holistic study. more...

Organism:

Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL7137

15 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; 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; 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; 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

Type:

Methylation profiling by high throughput sequencing

228 related Platforms

237 Samples

Download data: CSV, GFF

(Submitter supplied) Mutants from SG511 and NCTC8325 (wild type isolates) resistant to daptomycin were obtained following serial passage experiments in vitro. Transcriptomic experiments showed alteration in the expression of genes involved in various pathways including general metabolism, cell wall regulon and lipid metabolism.

Organism:

Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus USA300; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus COL

Type:

Expression profiling by array

Platform:

GPL7137

4 Samples

Download data: TXT

(Submitter supplied) Little is known about the expression of methicillin-resistant Staphylococcus aureus (MRSA) genes during infection conditions. Here, we described the transcriptome of the clinical MRSA strain USA300 derived from human cutaneous abscesses, and compared it with USA300 bacteria derived from infected kidneys in a mouse model. Remarkable similarity between the transcriptomes allowed us to identify genes encoding multiple proteases and toxins, and iron- and peptide-transporter molecules, which are upregulated in both infections and are likely important for establishment of infection. more...

Organism:

Staphylococcus aureus subsp. aureus USA300_FPR3757; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL20994

16 Samples

Download data: TXT

(Submitter supplied) We report the transcriptome profiles (RNA seq) of three different co-isolates of S.aureus that have been identified and isolated in both laboratory and infective scenarios. The transcriptome profiles were generated by deep sequencing and transcript levels assessed. For this the raw reads underwent quality-trimming (using the FastX suite), polyA-clipping, size filtering, mapping to the reference genome, coverage calculation, gene wise expression quantification followed by differential gene expression analysis (all done by the tool "READemption" (Förstner et al., unpublished) using "segemehl" (Hoffmann et al., 2009) and "DESeq" (Anders et al., 2010). more...

Organism:

Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17544

3 Samples

Download data: WIG

(Submitter supplied) With a copy number of about 25,000 molecules per cell, Asp23 is one of the most abundant proteins in Staphylococcus aureus. Asp23 has been characterized as a protein with an apparent molecular mass of 23 kDa that, following an alkaline shock, accumulates in the soluble protein fraction. Moreover, it was shown that transcription of the asp23 gene is exclusively regulated by the alternative sigma factor B. more...

Organism:

Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL7137

12 Samples

Download data: TXT

(Submitter supplied) A mutant of SG511 (wild type isolate), resistant to the presence of chitosan (polycationic molecule) was obtained following serial passage experiments resistance to chitosan exposition. Transcriptomic experiments showed alteration in the expression of genes involved in the cell wall regulon resulting in the modification of susceptibility phenotype against cell wall active antibiotics

Organism:

Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus USA300; Staphylococcus aureus subsp. aureus MW2

Type:

Expression profiling by array

Platform:

GPL7137

3 Samples

Download data: TXT

(Submitter supplied) Compilation fo whole genome gene expression changes in Staphylococcus aureus USA300 LAC cultures grown in the presence of vehicle or the anti-gout drug benzbromarone. The drug was intially screened as effective against the agr quorum sensing system in Staphylococcus aureus AH1677.

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL18434

6 Samples

Download data: PAIR, XLSX

(Submitter supplied) S. aureus has the propensity to survive a range of NaCl challenge conditions We used commercially available Affymetrix S. aureus GeneChips (part number 900514) to compare the gene expression properties of wild type cells during growth at no or high (2M) NaCl.

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus USA300

Type:

Expression profiling by array

Platform:

GPL1339

4 Samples

Download data: CEL, CHP