GEO DataSets

(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) Analysis of the human monocyte-derived macrophage (hMDM) transcriptional response to L. pneumophila infection at 8 hours post-infection We used microarrays to probe the hMDM transcriptional response to wild type L. pneumophila AA100 infection and its isogenic ankB and T2SS mutants. We identified up-regulation of innate immunity pathways and down-regulation of protein translation pathways

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

12 Samples

Download data: CEL

(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) 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

Download data

(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

Download data

(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

Download data

(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) 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) To study the gene expression of wild-type L. longbeachae and a mutant in the capsule transporter gene ctrC, we grew each strain to exponential, post-exponential or stationary phase and extracted RNA for RNAseq.

Organism:

Legionella longbeachae NSW150

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34703

24 Samples

Download data: TXT

(Submitter supplied) Pathogens often secrete proteins or nucleic acids that mimic the structure and/or function of molecules expressed within their host counterparts. Such molecular mimicry empowers pathogens to subvert critical host processes and helps establish infection. We report here that the intracellular bacterium Legionella pneumophila (L.p.) secretes a toxin named SidI (substrate of icm/dot transporter I) which possesses a transfer RNA (tRNA) like fold and functions as a mannosyl transferase . more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 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

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

(Submitter supplied) Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts. To date, such studies have investigated primarily Bacteria. more...

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18473

5 Samples

Download data: WIG

(Submitter supplied) Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium TMC724. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these coincided with the start codons and therefore belong to leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. more...

Organism:

Mycobacterium avium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17051

1 Sample

Download data: TXT

(Submitter supplied) We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters.

Organism:

Streptomyces venezuelae; Streptomyces coelicolor; Streptomyces avermitilis

Type:

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

Platforms:

GPL17014 GPL17012 GPL17013

6 Samples

Download data: TXT

(Submitter supplied) We used RNA-Seq to experimentally annotate H. somni strain 2336 and construct a single nucleotide resolution transcriptome map. Novel expressed elements were identified, and where appropriate, computational predictions of previously described gene boundaries were corrected.

Organism:

Histophilus somni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13659

1 Sample

Download data: BED

(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 monocytogenes EGD-e; Listeria innocua Clip11262

Type:

Other

Platforms:

GPL15272 GPL15273

16 Samples

Download data: TXT

(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) Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). more...

Organism:

Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28094

24 Samples

Download data: WIG, XLSX

(Submitter supplied) The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3,217 strand-specific Transcriptionally Active Regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 81.5% of the genes as they are currently annotated and additionally we find 44 novel protein-coding genes, 85 putative non-coding RNAs (ncRNAs) and 184 antisense transcripts. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL8486

10 Samples

Download data: PAIR