GEO DataSets

(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) In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ΔBCHL Prha-sigH and ΔBCHL Prha. RNA-seq was performed on ΔBCHL Prha-sigH and ΔBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). more...

Organism:

Listeria monocytogenes 10403S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20912

6 Samples

Download data: TXT, XLSX

(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

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

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platforms:

GPL7821 GPL7822

295 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array

Platform:

GPL7822

252 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platform:

GPL7821

43 Samples

Download data

(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) 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) To understand physiological processes in vivo, it is vital to disclose the conformation of biological molecules inside living cells and correlate their structure with their function. Here, we describe a method, FUSE (5’-UTR Structure Elucidation) that was used to characterize changes in the structures of 5’-UTRs at different conditions inside the human bacterial pathogen Listeria monocytogenes. Using FUSE, we discovered a novel RNA thermoswitch and calculated the ratio of two conformations that this thermoswitch assumes at different conditions. more...

Organism:

Listeria monocytogenes EGD-e

Type:

Other

Platform:

GPL19076

10 Samples

Download data: XLSX

(Submitter supplied) Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min. The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. more...

Organism:

Listeria monocytogenes LO28; Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL18538

12 Samples

Download data: PAIR

(Submitter supplied) Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. more...

Organism:

Candida albicans

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10636 GPL10637

12 Samples

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) Riboswitches are ligand-binding elements contained within the 5’ untranslated regions of bacterial transcripts, which generally regulate expression of downstream open reading frames. Here we show that in Listeria monocytogenes, a Vitamin B12-binding (B12) riboswitch controls expression of a non-coding regulatory RNA, Rli55. Rli55 in turn controls expression of the eut genes, which enable ethanolamine utilization and require B12 as a cofactor. more...

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19076 GPL19075

8 Samples

Download data: TXT

(Submitter supplied) In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

22 Samples

Download data: WIG

(Submitter supplied) Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. more...

Organism:

Tiamatvirus PSSP7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9313; Prochlorococcus phage P-SSM4

Type:

Expression profiling by array

Platform:

GPL8853

5 Samples

Download data: CEL, TXT

(Submitter supplied) The obligate intracellular human pathogen Chlamydia pneumoniae was subjected to dRNA-Seq to gain insights into the transcriptome. The two distinct life cycle forms elementary bodies (EB) and reticulate bodies (RB) were isolated from human Hep2 cell line by differential gradient centrifugation.

Organism:

Chlamydia pneumoniae CWL029

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11140

8 Samples

Download data: TXT

(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) 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 FSL F2-515; Listeria monocytogenes FSL J2-071; Listeria monocytogenes J0161; Listeria monocytogenes HPB2262; Listeria monocytogenes FSL F2-208; 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 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 serotype 4b str. H7858; Listeria monocytogenes FSL J1-208; Listeria monocytogenes FSL N3-165; Listeria monocytogenes LO28

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8942

18 Samples

Download data: PAIR, TXT

(Submitter supplied) Background: Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Methylotrophy in this organism depends on the endogenous plasmid pBM19 although all ribulose monophosphate cycle enzymes are also encoded on the chromosome. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising and valuable candidate for future biotechnological applications is evident. more...

Organism:

Bacillus methanolicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19581

2 Samples

Download data: XLS