GEO DataSets

(Submitter supplied) We report the use of Next Generation RNA Sequencing for confirming or improving initial identification of small regulatory RNA in Staphylococcus aureus to prodive a list of the most probable RNA molecules transcribed as independent units.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19531

6 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) In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19476

4 Samples

Download data: XLS

(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 epidermidis; Staphylococcus aureus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21408 GPL19476 GPL21407

3 Samples

Download data: XLSX

(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) 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) 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) 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) Small RNAs are emerging as important molecules for cross-species communication. Thanks to available and affordable sequencing technologies it is now possible to sequence small RNAs (sRNA-Seq) present in samples of interacting organisms. A first step when analyzing sRNA-Seq of two interacting species is to determine which sequences are being produced by which organism. Due to their small size (18-30), small RNAs could easily map to both host and parasite genomes. more...

Organism:

Mus musculus; Heligmosomoides polygyrus bakeri

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25995 GPL21103

12 Samples

Download data: TXT

(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:

GPL19531 GPL25144

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) 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) Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within the adverse soil environment. more...

Organism:

Pectobacterium atrosepticum SCRI1043

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20147

2 Samples

Download data: TAB, XLSX

(Submitter supplied) Our aims in this study were: 1) to identify the miRNAs of the bumble bees Bombus terrestris and B. impatiens; 2) to compare the total numbers of miRNAs between both bumble bee species and between them and the honey bee, Apis mellifera; and 3) to test whether the sequences and expression patterns of miRNAs were conserved between species. To investigate each of these aims we used miRNA-seq (deep sequencing of miRNA-enriched libraries) in B. more...

Organism:

Bombus terrestris

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19585

8 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen. S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (Methicillin-resistant S. aureus) strains. Here we present a method to study differential gene expression in S. aureus using high-throughput RNA-sequencing (RNA-seq). We use RNA-seq to examine the differential gene expression in S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

3 Samples

Download data: WIG

(Submitter supplied) in vitro comparison between two MRSA grown in rich (BHI) and poor media (SNM), compared with the nasal metatranscriptome reads of S. aureus.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18481 GPL16057

7 Samples

Download data: TXT

(Submitter supplied) The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non coding RNAs (sRNAs). Most of the sRNAs regulate gene expression through base-pairings with mRNAs. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19006

6 Samples

Download data: XLSX

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

Organism:

Streptococcus pyogenes

Type:

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

Platforms:

GPL6186 GPL9080

15 Samples

Download data: CEL