GEO DataSets

(Submitter supplied) RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of a 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma, and by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16nt). more...

Organism:

synthetic construct; Salmonella enterica subsp. enterica serovar Typhimurium; Pseudomonas aeruginosa PA7; Legionella pneumophila; Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

12 Samples

Download data: FA, PDF

(Submitter supplied) Legionella pneumophila Philadelphia-1 strain was grown to stationary phase in AYE broth and starved in freshwater for 2 hours and RNA was harvested with or without sublethal heat shock via immersion in a 55 degree C hot water bath for 5 minutes

Organism:

Legionella pneumophila subsp. pneumophila ATCC 33215; Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

6 Samples

Download data: TXT

(Submitter supplied) Extracellular vesicles (EVs) produced by bacteria, archaea and eukaryotic cells, are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. To characterize the effect of Lp-EVs on THP-1 cells, in particular the immune response, three independent RNAseq libraries were constructed from from THP-1 cells non-infected, incubated with purified wt-EVs or with purified EV from delta-rsmY Legionella bacteria. more...

Organism:

Legionella pneumophila; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL31034

9 Samples

Download data: TXT

(Submitter supplied) Extracellular vesicles (EVs) produced by bacteria, archaea and eukaryotic cells, are increasingly recognized as important mediators of intercellular communication via transfer of a wide variety of molecular cargoes. To characterize and identify the RNA molecules enriched in Legionella pneumophila extracellular vesicles (Lp-EVs) we performed RNAseq analyses. Four independent RNAseq libraries were constructed from RNA isolated from purified Lp-EVs and as control from the bacterial pellets, from which the Lp-EVs had been shed and deep sequenced using an Illumina platform. more...

Organism:

Legionella pneumophila

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26128 GPL29224

8 Samples

Download data: TXT

(Submitter supplied) The intracellular pathogen Legionella pneumophila (Lp) is a strict aerobe, surviving and replicating in environments where it frequently encounters reactive oxygen species, such as the nutrient-poor water environment and inside host cells. In many proteobacteria, the oxidative stress response is regulated by the LysR-type regulator OxyR; however, the role played by the OxyR homologue in Lp is still unclear. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

12 Samples

Download data: TXT

(Submitter supplied) Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. more...

Organism:

Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; Helicobacter pylori; Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) Diversity-generating retroelements (DGRs) function through a mutagenic retrohoming mechanism that introduces localized nucleotide substitutions in genes. Throught transcriptional profiling of the DGR genes and host global regulatory networks, here we probe how tight host-control over DGR activity balances the benefit of localized protein diversification with the potential loss of fitness from unbridled mutagenesis.

Organism:

Legionella pneumophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27897

16 Samples

Download data: XLSX

(Submitter supplied) Legionella pneumophila (Lp) is a waterborne bacterium able to infect human alveolar macrophages, causing a severe pneumonia known as Legionnaires’ disease. In water, Lp grows inside ciliates and ameoba. Lp is able to survive for several months in water, while searching for host cells. In Lp, the sigma factor RpoS is important for survival in water. Several small regulatory RNAs (sRNA) are known to regulate the expression of RpoS in other bacteria. more...

Organism:

Legionella pneumophila subsp. pneumophila; Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

9 Samples

Download data: TXT, XLS

(Submitter supplied) Legionella pneumophila are important opportunistic pathogens for which environmental reservoirs such as protists are crucial for the infection of humans. Free-living amoebae are considered key hosts providing nutrients and shelter for highly efficient intracellular proliferation of L. pneumophila, which eventually leads to lysis of the amoeba host cell. Yet, the significance of other bacterial players for L. more...

Organism:

Acanthamoeba castellanii; Legionella pneumophila; Candidatus Protochlamydia amoebophila

Type:

Expression profiling by high throughput sequencing

4 related Platforms

22 Samples

Download data: TXT

(Submitter supplied) Surviving the nutrient-poor aquatic environment for extended periods of time is important for transmission of various water-borne pathogen to the host, including Legionella pneumophila (Lp). Lp is a leading cause of community-acquired and nosocomial pneumonia called Legionnaires’ disease. The remarkable ability of the bacterium to survive in water for periods ranging from several months to years under starvation conditions alludes to regulatory pathways that mediate adaptation to the water environment. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

12 Samples

Download data: TXT

(Submitter supplied) The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. The goal of the study was to use deep sequencing of RNA enriched by co-immunoprecipitation with epitope tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 478 mRNAs or non-coding RNAs to be targets of CsrA. more...

Organism:

Legionella pneumophila str. Paris

Type:

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

Platform:

GPL22984

10 Samples

Download data: WIG

(Submitter supplied) The bacterium Legionella pneumophila is capable of intracellular replication within freshwater protozoa as well as human alveolar macrophages, the latter of which results in the serious pneumonia Legionnaires’ disease. A primary factor involved in these host cell interactions is the Dot/Icm Type IV secretion system that is responsible for translocating effector proteins needed to establish and maintain the bacterial replicative niche. more...

Organism:

Legionella pneumophila; Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

12 Samples

Download data: TXT

(Submitter supplied) Legionella pneumophila is a water-borne pathogen, and thus survival in the aquatic environment is central to its transmission to humans. Hence, identifying genes required for its survival in water could help prevent Legionnaires’ disease outbreaks. In the present study, we investigate for the first time the role of the sigma factor RpoS in promoting the survival in water, where L. pneumophila experiences total nutrient deprivation. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL18472

12 Samples

Download data: TXT

(Submitter supplied) Legionella pneumophila (Lp) is an opportunistic pathogen and its survival in water is critical for human infection. Therefore, identifying the genes of Lp that are required for survival in water may help devise strategies to prevent Legionella outbreaks. In this study, we exposed Lp in rich medium and in an artificial freshwater medium (Fraquil) for 2, 6 and 24 hours to uncover the global transcriptomic changes of Lp in water. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL19458

12 Samples

Download data: TXT

(Submitter supplied) In this report, we have developed a rapid oligonucleotide microarray detection technique to identify the most common ten Legionella spp.. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven air conditioner-condensed water samples with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. more...

Organism:

Legionella micdadei; Legionella jordanis; Fluoribacter dumoffii; Fluoribacter gormanii; Legionella maceachernii; Legionella anisa; Legionella pneumophila; Legionella bozemanae; Legionella longbeachae; Legionella fairfieldensis; Legionella

Type:

Genome variation profiling by array

Platform:

GPL19258

14 Samples

Download data: GPR

(Submitter supplied) Legionella pneumophila wild-type and hfq mutant were grown to post-exponential. The wild-type strain is used as the control.

Organism:

Legionella pneumophila; Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL7283

6 Samples

Download data: CSV

(Submitter supplied) Legionella pneumophila was exposed for 3h to 160 ug/ml of CuO nanoparticle. Untreated samples are used as the control condition.

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1; Legionella pneumophila

Type:

Expression profiling by array

Platform:

GPL7283

6 Samples

Download data: CSV

(Submitter supplied) Legionella pneumophila is a Gram-negative facultative intracellular human pathogen with a distinct biphasic lifestyle. One of its primary environmental hosts in the free-living amoeba Acanthamoeba castellanii and its infection by L. pneumophila mimics that seen in human macrophages. Here we present analysis of strand specific sequencing of the transcriptional response of L. pneumophila in broth growth and in infection of A. more...

Organism:

Legionella pneumophila

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13156

5 Samples

Download data: BED

(Submitter supplied) Legionella pneumophila is the causative agent of Legionnaires’ disease, an acute pulmonary infection. L. pneumophila is able to infect and multiply in both phagocytic protozoan, such as Acanthamoeba castellanii, and mammalian professional phagocytes. The best-known virulence determinant used by L. pneumophila to infect host cells is a Type IVb translocation system named Icm/Dot, which is used to modify the host cell functions to the benefit of the bacteria. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL7283

12 Samples

Download data

(Submitter supplied) Legionella pneumophila is the causative agent of Legionnaires’ disease, an acute pulmonary infection. L. pneumophila is able to infect and multiply in both phagocytic protozoan, such as Acanthamoeba castellanii, and mammalian professional phagocytes. The best-known virulence determinant used by L. pneumophila to infect host cells is a Type IVb translocation system named Icm/Dot, which is used to modify the host cell functions to the benefit of the bacteria. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL7283

30 Samples

Download data