GEO DataSets

(Submitter supplied) For bacteria in general and Listeria monocytogenes in particular, little is known about transcriptome diversity in comparison to the copious data on intraspecific genome diversity. The current study employed RNA sequencing to investigate the variation of transcript levels of conserved single copy genes from several perspectives including differences between lineages and correlation with previous classification of the virulence potential of clonal complexes based on epidemiological MLST data. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26477

66 Samples

Download data: CSV

(Submitter supplied) Listeria monocytogenes strains classify into at least three distinct phylogenetic lineages. Correlations exist between lineage classification and source of bacterial isolation, e.g., human clinical and food isolates usually classify into either lineage I or II, however, human clinical isolates are over-represented in lineage I while food isolates are over-represented in lineage II. σB, a transcriptional regulator previously demonstrated to contribute to environmental stress response and virulence in L. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL4281

4 Samples

Download data: GPR

(Submitter supplied) The aim of this study is to contribute to the understanding of L. monocytogenes virulence and survival capabilities using global gene expression profiling by means of DNA macroarrays. Keywords: strain comparison; correlation between expression and behaviour

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL2811

24 Samples

Download data

(Submitter supplied) According to Doumith et al (2004, Infect Immun. 72:1072–1083): MATERIALS AND METHODS - Probe selection, primer design, PCR amplification, and array construction. The L. monocytogenes EGDe-specific probes spotted onto the Listeria array corresponded to the 270 genes defined previously as being specific for L. monocytogenes EGDe with respect to L. innocua CLIP 11262. As some genes were too small to allow amplification of a PCR product of optimal size, the final array contained 262 EGDe genes. more...

Organism:

Listeria monocytogenes

1 Series

24 Samples

Download data

(Submitter supplied) Time course study of the mouse infection by comparing the genomic transcriptional patterns of Listeria monocytogenes EGDe grown under laboratory conditions (exponential growth phase) with that of in vivo-grown bacteria (in mouse spleens) over three days of infection.

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by array

Platform:

GPL7248

8 Samples

Download data

(Submitter supplied) Microbial population heterogeneity allows for a differential microbial response to environmental stresses and can lead to the selection of stress resistant variants. In this study, we have used two different stress resistant variants of Listeria monocytogenes LO28 with mutations in the rpsU gene encoding ribosomal protein S21, to elucidate features that can contribute to fitness, stress-tolerance and host interaction using a comparative gene profiling and phenotyping approach. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes LO28

Type:

Expression profiling by array

Platform:

GPL25009

10 Samples

Download data: TXT

(Submitter supplied) Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high fatality rate among infected, immuno-compromised individuals. Three genetic lineages have been identified within this species. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes EGD-e; Listeria monocytogenes serotype 4b str. F2365; Listeria monocytogenes serotype 1/2a str. F6854; Listeria monocytogenes FSL J1-175; Listeria monocytogenes FSL R2-503; Listeria monocytogenes J2818; Listeria monocytogenes serotype 4b str. H7858; Listeria monocytogenes FSL J1-208; Listeria monocytogenes FSL N3-165; Listeria monocytogenes LO28; Listeria monocytogenes FSL J1-194; Listeria monocytogenes FSL J2-003; Listeria monocytogenes FSL J2-064; Listeria monocytogenes FSL N1-017; Listeria monocytogenes F6900; Listeria monocytogenes 10403S; Listeria monocytogenes FSL F2-515; Listeria monocytogenes FSL J2-071; Listeria monocytogenes J0161; Listeria monocytogenes HPB2262; Listeria monocytogenes FSL F2-208

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8942

18 Samples

Download data: PAIR, TXT

(Submitter supplied) Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ3] Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ1] Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 Samples

Download data: TXT

(Submitter supplied) Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. more...

Organism:

Listeria innocua Clip11262; Listeria monocytogenes EGD-e

Type:

Other

Platforms:

GPL15272 GPL15273

16 Samples

Download data: TXT

(Submitter supplied) The foodborne pathogen Listeria monocytogenes (Lm) can cause invasive infection in susceptible animals and humans. To survive and proliferate within hosts, this facultative intracellular pathogen needs to tightly coordinate the expression of a complex regulatory network, including virulence factors. Here, we identify and characterize MouR a novel virulence regulator of Lm. Through RNA-seq transcriptomic analysis, we characterized the MouR regulatory network and demonstrated how MouR positively controls the expression of the Agr system (agrBDCA) of Lm. more...

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24263

6 Samples

Download data: TXT

(Submitter supplied) The stationary phase stress response transcriptome of the human bacterial pathogen Listeria monocytogenes was defined using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic DsigB mutant, which does not express the alternative sigma factor σB, a major regulator of genes contributing to stress response. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9363

4 Samples

Download data: TXT

(Submitter supplied) Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: FASTA, TXT

(Submitter supplied) The Gram-positive bacterium Listeria monocytogenes is widely distributed in the environment and capable of causing food-borne infections in susceptible individuals. In this study, we investigated the cell envelope stress response in L. monocytogenes. Whole-genome transcriptional profiling was performed to investigate the response upon exposure to the cell wall antibiotic cefuroxime. Differential expression (≥ 2-fold difference) of 558 genes was observed, corresponding to 20% of the L. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes EGD-e

Type:

Expression profiling by array

Platform:

GPL14687

16 Samples

Download data: TXT

(Submitter supplied) The enteric pathogen Yersinia enterocolitica is a the most common gram-negative zoonotic pathogen that causes a variety of gut-associated diseases named yersiniosis ranging from enteritis, watery diarrhea, mesenteric lymphadenitis to post infectious extraintestinal sequelae such as reactive arthritis human yersiniosis. The species Y. enterocolitica comprises a diverse group of about 70 serotypes of which only 11 are harmful to humans. more...

Organism:

Yersinia enterocolitica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19851

56 Samples

Download data: TXT

(Submitter supplied) Alkali stress is an important means of inactivating undesirable pathogens in a wide range of situations, ranging from environmental cleaning of food processing environments, to the phagolysosomal killing of cells engulfed by mammalian phagocytes. Unfortunately, L. monocytogenes can launch an alkaline tolerance response (AlTR), significantly increasing persistence of the pathogen in such environments. more...

Organism:

Listeria monocytogenes 10403S; Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL5170

4 Samples

Download data: TAV

(Submitter supplied) Genome-wide transcriptional responses of Yersinia entomophaga to shifts in temperature (25 - 37 degrees C) and in vitro and in vivo growth conditions were investigated using RNA-seq.

Organism:

Yersinia entomophaga

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27945

24 Samples

Download data: TXT

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

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24880

750 Samples

Download data

(Submitter supplied) Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations. Methods: An isogenic mutant strain (MGAS27961-10T) with a 10-T homopolymeric tract was generated using allelic exchange. Primers were used to amplify a 2,690-bp fragment using genomic DNA of MGAS28085 an emm28 clinical isolate with the naturally occurring 10 “T” variant region. more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24880

12 Samples

Download data: TXT

(Submitter supplied) Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations. Methods: We chose a subset of isolates from the sequenced population of 2,101 emm28 strains that would approximately span the genetic variation present in the entire population. more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24880

296 Samples

Download data: TXT