GEO DataSets

(Submitter supplied) Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. more...

Organism:

Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2; Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus USA300; Staphylococcus aureus subsp. aureus MRSA252

Type:

Non-coding RNA profiling by array

Platform:

GPL7137

2 Samples

Download data: TXT

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

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16057 GPL24214

14 Samples

Download data

(Submitter supplied) Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24214

10 Samples

Download data: TXT

(Submitter supplied) Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16057

4 Samples

Download data: CSV, GFF

(Submitter supplied) We performed differential RNA-seq of two Staphylococcus epidermidis clinical isolates (PS2 and PS10) to compare their transcription profiles. The isolates were originally obtained from blood cultures during a systemic infection in an immunocompromised patient (Weisser et al. 2010. J Clin Microbiol 48: 2407-2412). They are of clonal origin, but differ phenotypically with respect to extracellular biofilm matrix production. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26150

4 Samples

Download data: WIG

(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) We used this array as described in Babak, Blencowe, anf Hughes (2005), to screen novel ncRNA predictions. See author supplementary data for more detailed probe information. Keywords: parallel sample

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL1896

16 Samples

Download data

(Submitter supplied) We used high-throughput methods to discover the Salmonella RNAs that are targeted by the bacterial Sm-like protein, Hfq. Our generic approach, using chromosomal epitope tagging and coIP-on-chip will also be useful to identify the post-transcriptional regulons of many other RNA-binding proteins. Keywords: coIP-chip

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica

Type:

Other

Platform:

GPL5791

4 Samples

Download data: TXT

(Submitter supplied) The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification

Organism:

Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL5780

12 Samples

Download data: TXT

(Submitter supplied) The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3,217 strand-specific Transcriptionally Active Regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 81.5% of the genes as they are currently annotated and additionally we find 44 novel protein-coding genes, 85 putative non-coding RNAs (ncRNAs) and 184 antisense transcripts. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL8486

10 Samples

Download data: PAIR

(Submitter supplied) To understand functional roles of ncRNAs during exponential growth phase, we captured transcriptome changes by conducting strand-specific RNA-seq.

Organism:

Kluyveromyces marxianus

Type:

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

Platform:

GPL20596

6 Samples

Download data: GFF, TXT

(Submitter supplied) Endonucleolytic cleavage within polycistronic mRNAs can lead to differential stability and discordant abundance among co-transcribed genes. RNase Y, the major endonuclease for mRNA decay in Bacillus subtilis, was originally identified for its cleavage activity towards the cggR-gapA operon, an event that differentiates the expression of a glycolytic enzyme from its transcriptional regulator. A three-protein Y-complex (YlbF, YmcA, and YaaT) was recently identified that is also required for this cleavage in vivo, raising the possibility that it is an accessory factor acting to regulate RNase Y. more...

Organism:

Staphylococcus aureus; Bacillus subtilis

Type:

Other

Platforms:

GPL17452 GPL18561

16 Samples

Download data: WIG

(Submitter supplied) The expression profiling of 245 known and 82 novel imsRNAs (intermediate-size noncoding RNAs, 50-500nt, which were identified from human fetal brain tissue) across different human fetal tissues (brain, heart, liver, lung and spleen at the 24-week gestation stage), different fetal brain gestational stages (13w, 14w, 20w, and 24w) and two human brain tumor cell lines (SHSY-5Y and U251).

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL11342

22 Samples

Download data: GPR