GEO DataSets

(Submitter supplied) Transcriptomics by RNA-seq provides unparalleled insight into bacterial gene expression networks, enabling a deeper understanding of the regulation of pathogenicity, mechanisms of antimicrobial resistance, metabolism, and other cellular processes. Here we present the transcriptome architecture of Acinetobacter baumannii ATCC 17978, a species emerging as a leading cause of antimicrobial resistant nosocomial infections. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23966 GPL19442

5 Samples

Download data: GR

(Submitter supplied) Purpose: In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075. Methods: To further characterize the functional interactions between AdeABC and AdeIJK, we carried out RNAseq analysis of the exponential AB5075 and its single and double efflux knockout cells. High quality total RNA was further processed by removing 23S and 16S rRNAs using the MicrobExpress bacterial mRNA enrichment kit. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19442

8 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to assess the role of the AdeRS two component signal transduction system in Acinetobacter baumannii ATCC 17978 and its impact on the virulence potential of this bacterial organism. Specific gene deletion strains targeting the adeRS system were generated and compared to wildtype for a number of phenotypic in vitro assays as well as transcriptomic profiling via RNA-sequencing.

Organism:

Acinetobacter baumannii ATCC 17978

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23922

2 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiling of quorum sensing regulated genes in Acinetobacter baumannii 863

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19442

6 Samples

Download data: TXT

(Submitter supplied) We describe a novel genetic mechanism  in which tandem amplification of a plasmid-borne integron regulates virulence, opacity variation, and global gene expression by altering levels of a putative small RNA (sRNA) in Acinetobacter baumannii AB5075. Copy number of this amplified locus correlated with the rate of switching between virulent opaque (VIR-O) and avirulent translucent (AV-T) cells. We found that prototypical VIR-O colonies, which exhibit high levels of switching and visible sectoring with AV-T cells by 24 h of growth, encode two copies of this locus. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26038

6 Samples

Download data: TXT

(Submitter supplied) In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. more...

Organism:

Acinetobacter baumannii AB5075

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21208

1 Sample

Download data: XLSX

(Submitter supplied) Background Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps is the initiation of transcription. Identification of the first nucleotide transcribed by the RNA polymerase is therefore essential to understand the underlying regulatory processes, since this provides insight on promoter strength and binding sites for transcriptional regulators, and additionally reveals the exact 5' untranslated region of the transcripts, which often contains elements that regulate translation. more...

Organism:

Staphylococcus epidermidis; Acinetobacter baumannii; Staphylococcus aureus; Klebsiella aerogenes

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

30 Samples

Download data: TSV

(Submitter supplied) In this study transcriptional start sites (TSS) for H. pylori 26695 were determined

Organism:

Helicobacter pylori 26695

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19991 GPL19992

6 Samples

Download data: WIG

(Submitter supplied) A. baumannii ATCC 17978 cells were incubated under iron replete (mueller-hinton) and iron limiting (MH + 200 µM 2,2'-dipyridyl) conditions, total RNA was extracted when cultures reached OD600=0.7.

Organism:

Acinetobacter baumannii

Type:

Expression profiling by array

Platform:

GPL11113

4 Samples

Download data: TXT

(Submitter supplied) We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

Organism:

Actinobacillus pleuropneumoniae serovar 3 str. JL03

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20603

1 Sample

Download data: BED

(Submitter supplied) Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and a leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. more...

Organism:

Streptococcus pneumoniae D39

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25906

10 Samples

Download data: TXT

(Submitter supplied) Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and the leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. more...

Organism:

Streptococcus pneumoniae D39

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25906

6 Samples

Download data: BW

(Submitter supplied) Colistin is a crucial last-line drug used for the treatment of life-threatening infections caused by multi-drug resistant strains of the Gram-negative bacteria, Acinetobacter baumannii. However, colistin resistant A. baumannii isolates can be isolated following failed colistin therapy. Resistance is most often mediated by the addition of phosphoethanolamine (pEtN) to lipid A by PmrC, following missense mutations in the pmrCAB operon encoding PmrC and the two-component signal transduction system PmrA/PmrB. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19644

6 Samples

Download data: CSV, GFF

(Submitter supplied) Purpose: The goal of this study was to elucidate the collateral effects associated with OXA-23 overexpression on the Acinetobacter baumannii global transcriptome. Results: Besides the 99.73-fold increase in blaOXA-23 transcript upon IPTG induction, no other transcripts showed more than a 2-fold change compared to the wildtype control. This suggests that OXA-23 over expression to levels similarly observed in multi drug resistant A. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19644

6 Samples

Download data: TXT