GEO DataSets

(Submitter supplied) Legionella pneumophila is a gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to test the hypothesis that sRNAs play a similar role in L. pneumophila. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Expression profiling by array

Platform:

GPL7283

6 Samples

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

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

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

Platforms:

GPL9531 GPL7283

66 Samples

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(Submitter supplied) Legionella pneumophila is a gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to test the hypothesis that sRNAs play a similar role in L. pneumophila. more...

Organism:

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Type:

Non-coding RNA profiling by array

Platform:

GPL9531

60 Samples

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(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) Transcriptional profiling of L. pneumophila JR32 (wild-type) and rpoS- (LM1376) strains grown to stat phase compared to cultures grown to log phase Keywords: growth phase

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7283

2 Samples

Download data: CSV

(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 purpose of the study was to examine the role of the elements of PmrA/PmrB two-component system in the global regulation of gene expression in L.pneumophia during axenic growth. Towards this goal pmrA and pmrB isogenic mutants were constracted in L. pneumophila strain AA100 using allelic exchange. Gene expression profiles were generated for both mutants during their growth in axenic media and compared to the corresponding gene expression profiles in the ancestral strain.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7283

36 Samples

Download data: CSV

(Submitter supplied) We report here an experimental search for small non-coding RNAs in a low GC, gram-positive, human pathogenic bacteria Streptococcus pneumoniae. Based on the bioinformatic analyses by Livny et al. (2006, Nucleic Acids Res. 34:3484-93), we tested 36 candidates by Northern analyses and confirmed the expression of 8 novel and one previously-reported sRNAs (CcnA) in the genome of D39 serotype 2 strain. Some of the sRNAs showed differential expression in stationary phase or after treatment with competence stimulatory peptide compared to untreated exponential cells. One sRNA we detected is CcnA, one of five CiaR-controlled non-coding RNA (CcnA to E) reported previously. By ectopically expressing this sRNA in a ΔciaR strain, we provide evidence that CcnA plays important roles in the regulation of growth and chain length of S. pneumoniae. Microarray analysis comparing global gene expression of CcnA-expressing and CcnA-nonexpressing ΔciaR strains showed significant differences in expression of competence related genes and five putative transcriptional regulators. QPCR and transformation assays further confirmed that CcnA sRNA mediates a strong negative effect on competence development. Our findings suggested many of the CiaRH function may be mediated via Ccn sRNAs and that sRNAs play regulatory roles in S. pneumoniae, an organism that lacks Hfq RNA chaperone.

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by array

Platform:

GPL536

3 Samples

Download data: GPR

(Submitter supplied) We report the transcriptomic profile of Escherichia coli when the small RNA RydC is overexpressedand how this can be used to identify putative mRNA targets. This technique allowed us to identify potential mRNA targets to further validate in vivo.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

6 Samples

Download data: TXT, WIG

(Submitter supplied) This entry refers to transcriptome analysis of five E. coli strains: E. coli K-12 MG1655, single deletions of rsd, ssrS, and rpoS, as well as a double deletion of rsd and ssrS, in five growth phases.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15982

50 Samples

Download data: TXT

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that undergoes swarming motility in response to semisolid conditions with amino acids as a nitrogen source. With a genome encoding hundreds of potential intergenic small RNAs (sRNAs), P. aeruginosa can easily adapt to different conditions and stresses. We previously identified 20 sRNAs dysregulated under swarming conditions and here provide phenotypic characterization for these sRNAs. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

10 Samples

Download data: TXT

(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

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(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

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(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:

Legionella pneumophila; Candidatus Protochlamydia amoebophila; Acanthamoeba castellanii

Type:

Expression profiling by high throughput sequencing

4 related Platforms

22 Samples

Download data: TXT

(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) Purpose: The interaction between Legionella pneumophila and its host cell is not completly understood. The aim of this study was to identify eukaryotic-like bacterial factors which manipulate the host cell. Method: A stable overexpression of LPC_1677 was performed in THP-1 cells. The LPC_1677 overexpressing cells were infected with L.p. and RNA sequencing was performed. Key pro-inflammatory markers were validated via qPCR and ELISA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: XLSX

(Submitter supplied) Investigation of whole genome gene expression to identify overlooked sRNAs and sORFs. Background The completion of numerous genome sequences has introduced an era of whole-genome study. However, many real genes, including small RNAs (sRNAs) and small ORFs (sORFs), are missed in genome annotation. In order to improve genome annotation, we sought to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery or shigellosis. more...

Organism:

Shigella flexneri 2a str. 301

Type:

Expression profiling by genome tiling array

Platform:

GPL10653

15 Samples

Download data: PAIR

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

Organism:

Streptococcus pyogenes

Type:

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

Platforms:

GPL6186 GPL9080

15 Samples

Download data: CEL

(Submitter supplied) Small regulatory RNAs (sRNAs) represent a major mechanism of virulence regulation in several pathogens. To date, only three sRNAs have been described in GAS in any detail. To identify whether sRNAs are common within the GAS genome, we created a custom Affymetrix tiling microarray in which all intergenic regions (>49 bp) of the MGAS2221 genome were tiled at high density. Triplicate cultures of strain MGAS2221 in THY broth were grown to the exponential phase (O.D.600 of 0.5) of growth and RNA was isolated, converted to cDNA, fragmented, labeled, and hybridized to our custom array (one array per RNA sample [ hence three arrays total]). more...

Organism:

Streptococcus pyogenes

Type:

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

Platform:

GPL6186

3 Samples

Download data: BAR, CEL

(Submitter supplied) PEL is a small regulatory RNA that is present within the S. pyogenes genome. In some strains of S. pyogenes, the PEL sRNA regulates many of the known virulence factors produced by this pathogen. A genome-wide analysis of PEL-regulated genes had not been performed previously so we analyzed this by comparing the parental M1T1 isolate MGAS2221 with an isogenic PEL mutant. Comparing gene transcript levels between these two strains at the exponential and stationary phases of growth, we identified that PEL has no regulatory function in MGAS2221.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL9080

12 Samples

Download data: CEL