GEO DataSets

(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 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) 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) 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) 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) Background: The human pathogen Corynebacterium diphtheriae is the causative agent of the disease diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced several years ago, not much is known about the transcriptome. Our aim was to use RNA Sequencing to close this knowledge gap and gain insights into the transcriptional landscape of C. more...

Organism:

Corynebacterium diphtheriae NCTC 13129

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23376

7 Samples

Download data: XLSX

(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) Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. more...

Organism:

Staphylococcus carnosus; Staphylococcus aureus; Staphylococcus epidermidis

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21408 GPL19476 GPL21407

3 Samples

Download data: XLSX

(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 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) The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. more...

Organism:

Oryza sativa; Pyricularia oryzae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9316 GPL16451

8 Samples

Download data: 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

(Submitter supplied) High-density tiling microarray and RNA sequencing technologies were used to analyze the transcriptome of Porphyromonas gingivalis. The compiled P. gingivalis transcriptome were based on total RNA samples isolated from three different laboratory culturing conditions and the strand-specific transcription profiles generated covered the entire genome including both protein coding and non-coding regions. more...

Organism:

Porphyromonas gingivalis W83

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13827

3 Samples

Download data: TXT

(Submitter supplied) This data contained within this entry was produced as part of a study that included differential RNA-sequencing and microarray analysis. The results of the latter two have also been deposited in GEO

Organism:

Cutibacterium acnes KPA171202

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17154

2 Samples

Download data: TXT

(Submitter supplied) The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO.

Organism:

Cutibacterium acnes KPA171202

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17147

4 Samples

Download data: TXT