GEO DataSets

(Submitter supplied) Comparative Genomic and Transcriptomic Characterization of Colistin-Resistant Acinetobacter baumannii

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19442

8 Samples

Download data: XLSX

(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) Small RNAs are the non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs that has been carried out in various plant growth promoting bacteria have shown to help the bacterial cell cope up with environmental stress. more...

Organism:

Azospirillum baldaniorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25390

2 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) We report the transcriptional expression from wild type, a ponA mutant, and lipooligosaccharide-deficient A. baumannii in order to understand the cellular changes after inactivation of lipid A biosynthesis. Among all strains, genes in the Localization Of Lipoprotein (Lol) transport pathway were upregulated. This study provides a framework to understand how some Acinetobacter baumannii strains can survive without lipid A and lipopolysaccharide/lipooligosaccharide.

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22143

9 Samples

Download data: XLS

(Submitter supplied) We present the first genome-wide identification and characterizaion of 422 novel sRNAs in R. capsulatus. In addition we report a comparative analysis of conserved sRNAs across 24 bacterial species.

Organism:

Rhodobacter capsulatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20771

2 Samples

Download data: XLS

(Submitter supplied) Regulatory RNAs (sRNAs) are now considered as major players in many physiological and adaptive responses in pathogenic bacteria. sRNAs have been extensively studied in Gram-negative bacteria, but less information is available in Gram-positive pathogens. There is a spread of multidrug-resistant (MDR) opportunistic organisms, grouped as “ESKAPE” pathogens, which comprise enterococci, a leading cause of hospital-acquired infections and outbreaks with emergence of MDR isolates, especially vancomycin-resistant Enterococcus faecium (VREF). more...

Organism:

Enterococcus faecium Aus0004

Type:

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

Platform:

GPL23028

4 Samples

Download data: TXT

(Submitter supplied) Daptomycin (DAP) is the last-resort treatment for heterogeneous Vancomycin-Intermediate-Staphylococcus aureus (hVISA) and Vancomycin-Intermediate-S.aureus (VISA), and DAP-resistance onset which is also linked to reduced vancomycin susceptibility, is an increasing public health problem. To have more insight into the mechanisms of daptomycin resistance, the comparative transcriptomes of two DAP-R (1C-3B) clinical isogenic isolates vs their DAP-S (1A-3A) counterparts were investigated by Illumina RNA-seq, the Rockhopper tool, computational filtering analyses and bioinformatic tools.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18481

8 Samples

Download data: XLS

(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 SuperSeries is composed of the SubSeries listed below.

Organism:

Staphylococcus aureus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25144 GPL19531

14 Samples

Download data: TXT

(Submitter supplied) We have studied the transcriptome of S. aureus HG003 strain and HG003 DsarA strain

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19531

12 Samples

Download data: TXT

(Submitter supplied) ChIP seq for SarA in S. aureus HG003 wild type and HG003 DsarA

Organism:

Staphylococcus aureus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25144

2 Samples

Download data: TXT

(Submitter supplied) We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. more...

Organism:

Haloferax volcanii DS2

Type:

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

Platform:

GPL21976

16 Samples

Download data: TXT

(Submitter supplied) We report the use of Next Generation RNA Sequencing to identifiy novel sRNAs in the human pathogen Staphylococcus aureus

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18481 GPL19531

10 Samples

Download data: TXT

(Submitter supplied) Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

21 Samples

Download data: TXT, XLSX

(Submitter supplied) Accurate annotation of regulatory RNAs is a complex task but nevertheless essential as sRNA molecular and functional studies ensue from it. Several formerly considered small RNAs (sRNA) are now known to be parts of UTR transcripts. In light of experimental data, we review hundreds of Staphylococcus aureus putative regulatory RNAs. We pinpoint those that are likely acting in trans and are not expressed from the opposite strand of a coding gene. more...

Organism:

Staphylococcus aureus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16057

1 Sample

Download data: GFF

(Submitter supplied) High-throughput small RNA sequencing (sRNA-seq) has facilitated many discoveries, but extracellular sRNA (ExRNA) present unique analytical challenges that are not met by current software. Therefore, we developed a novel data analysis pipeline entitled, “TIGER”, which caters to exRNA. To demonstrate the power of this tool, sRNA-seq was performed on high-density lipoproteins (HDL), apolipoprotein B particles (APOB), bile, urine, and liver samples. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

66 Samples

Download data

(Submitter supplied) sRNAs represent a powerful class of regulators that influence multiple mRNA targets but remain largely uncharacterized outside of model organisms. Zymomonas mobilis is a natural ethanol-producing bacterium in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that sRNAs Zms4 and Zms6 have significant impacts on ethanol tolerance in Z. more...

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24294

21 Samples

Download data: GFF

(Submitter supplied) The induction of Z. mobilis sRNAs Zms4 and Zms6 reveals their regulatory impacts on gene networks.

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24294

12 Samples

Download data: GFF

(Submitter supplied) The MS2-affinity purification coupled to RNA-sequencing (MAPS) approach was used to identify RNA targets that physically associate in vivo with Zymomonas mobilis small RNAs Zms4 and Zms6.

Organism:

Zymomonas mobilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24294

9 Samples

Download data: GFF