GEO DataSets

Analysis of group A Streptococcus M3 strains MGAS315 and MGAS9887. MGAS9887 is underrepresented among necrotizing fasciitis cases and has a truncated MtsR transcriptional regulator. Results provide insight into the molecular basis of the differences in virulence between the strains.

Organism:

Borreliella burgdorferi; Yersinia pestis; Coxiella burnetii; Chlamydia trachomatis; Staphylococcus aureus; Streptococcus pyogenes; Streptococcus sp. 'group A'

Type:

Expression profiling by array, count, 2 strain sets

Platform:

GPL2129

Series:

GSE3966

12 Samples

Download data: CEL, EXP

(Submitter supplied) Epidemiological data indicate that strains MGAS315 and MGAS9887 differ significantly in their capacity to cause necrotizing fasciitis infections. To probe the hypothesis that this difference was associated with differences in gene expression, an expression MA comparison of the strains in exponential phase growth in rich media was conducted. Keywords: strain comparison

Organism:

Yersinia pestis; Streptococcus sp. 'group A'; Coxiella burnetii; Streptococcus pyogenes; Borreliella burgdorferi; Chlamydia trachomatis; Staphylococcus aureus

Type:

Expression profiling by array

Dataset:

GDS2353

Platform:

GPL2129

12 Samples

Download data: CEL, EXP

(Submitter supplied) Manuscript title: The endopeptidase PepO regulates the SpeB cysteine protease and is essential for the virulence of invasive M1T1 Streptococcus pyogenes. The study investigates the effect of pepO mutation on global gene expression in GAS M1T1 strain 5448.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL19152

3 Samples

Download data: TXT, XLSX

(Submitter supplied) RNA-seq experiments of a wild-type and isogenic rocA deletion mutant serotype M28 group A streptococcus strain at two time points

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24880

12 Samples

Download data: XLSX

(Submitter supplied) We used RNA-Seq to compare gene expression between representative serotype M1 and M3 GAS isolates

Organism:

Streptococcus pyogenes serotype M1; Streptococcus pyogenes serotype M3

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23320 GPL23321

6 Samples

Download data: XLSX

(Submitter supplied) We sequenced mRNA transcripts from three isogenic M3 serotype GAS strains, parental (MGAS10870), complement (10870::rocAM1), and deletion (10870ΔrocA). There were no significant changes between the parental and revertant strain. Comparison of the parental and complemented strain revealed several virulence factors were up-regulated in the parental strain where RocA function was diminished. We concluded that RocA, through direct or indirect mechanisms, is able to control numerous virulence genes and this lack of RocA regulation increases expression of virulence factors, which contributes to the hyper-virulent state of serotype M3 GAS.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19982

3 Samples

Download data: XLSX

(Submitter supplied) S. pyogenes strains were compared with the intact covRS form of the globally disseminated M1T1 clone to track transcriptomic changes engendered during the emergence of the M1T1 clone. The mutant covRS form of the M1T1 clone was included as a transcriptomic outlier and to provide a context for the magnitude of transcriptional shifts detected within the isolate set examined.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL10822

36 Samples

Download data: GPR

(Submitter supplied) The goal was to perform global transcriptome analysis on genetically representaive pre-epidemic and epidemic M89 strains to investigate how the genetic differnces may have altered gene expression potentially contributing to epidemic emergence and persistence.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20656

36 Samples

Download data: XLSX

(Submitter supplied) The goal was to perform global transcriptome analysis on isogenic wild type 2221 and FabT deletion mutant M1 strains to investigate how inactivation of the fabT gene affects gene expression.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20656

24 Samples

Download data: XLSX

(Submitter supplied) Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological phenotypes. To further our understanding of the molecular basis for ecological phenotypes, comparative genomic hybridization of a set of 97 diverse strains to a GAS pan-genome microarray was undertaken, and the association of accessory genes with emm genotypes that define tissue tropisms for infection was determined. more...

Organism:

Streptococcus sp. 'group A'

Type:

Genome variation profiling by array

Platform:

GPL14371

97 Samples

Download data: MEV

(Submitter supplied) RATIONALE: mtsR is a regulator of genes involved in ion aquisition in S. pyogenes that has been suggested to be involved in development of invasive infections. We wanted to identify mtsR regulon. EXPERIMENT: We compared global gene expression in wild type strain MGAS315 with expression in its isogenc mtsR mutant. Experiment was performed with bacteria in exponential (EXP) and at late exponential phase (Late EXP) grown in THY medium Keywords: strain comparison

Organism:

Coxiella burnetii; Chlamydia trachomatis; Streptococcus pyogenes; Borreliella burgdorferi; Yersinia pestis; Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL2129

12 Samples

Download data: CEL, CHP

(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

(Submitter supplied) Small regulatory RNAs (sRNAs) represent a major mechanism of virulence regulation in several pathogens. To date, only three sRNAs have been described in GAS in any detail. To identify whether sRNAs are common within the GAS genome, we created a custom Affymetrix tiling microarray in which all intergenic regions (>49 bp) of the MGAS2221 genome were tiled at high density. Triplicate cultures of strain MGAS2221 in THY broth were grown to the exponential phase (O.D.600 of 0.5) of growth and RNA was isolated, converted to cDNA, fragmented, labeled, and hybridized to our custom array (one array per RNA sample [ hence three arrays total]). more...

Organism:

Streptococcus pyogenes

Type:

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

Platform:

GPL6186

3 Samples

Download data: BAR, CEL

(Submitter supplied) PEL is a small regulatory RNA that is present within the S. pyogenes genome. In some strains of S. pyogenes, the PEL sRNA regulates many of the known virulence factors produced by this pathogen. A genome-wide analysis of PEL-regulated genes had not been performed previously so we analyzed this by comparing the parental M1T1 isolate MGAS2221 with an isogenic PEL mutant. Comparing gene transcript levels between these two strains at the exponential and stationary phases of growth, we identified that PEL has no regulatory function in MGAS2221.

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL9080

12 Samples

Download data: CEL

(Submitter supplied) Recent whole-genome sequencing of large populations of the same bacterial species has revealed significant disparity among genes in the frequency of single nucleotide polymorphisms (SNPs). For example, a previous analysis of invasive serotype M3 group A streptococci (GAS) found the highest frequency of SNPs in the gene (ropB) encoding the regulator of proteinase B (RopB). This finding led us to hypothesize that RopB polymorphisms contribute to altered GAS host-pathogen interactions. more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by array

Platform:

GPL9080

8 Samples

Download data: CEL

(Submitter supplied) We investigated the covS-regulation of S. pyogenes in a hypervirulent M23 strain using RNA-sequencing. The differential gene expression comparison between the covS- mutant and isogenic wild type covS+ identified altered expression of 349 (18%) genes, including a broad spectrum of virulence genes and diverse metabolic genes. The data showed that the strain achieved hypervirulence by enhancing the expression of genes responsible for invasiveness and antiphagocytosis (i.e., hasABC), by abrogating the expression of toxic genes (i.e., speB), and by compromising gene products with dispensable functions (i.e., sfb1). more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19982

8 Samples

Download data: XLS

(Submitter supplied) The molecular genetic mechanisms used by bacteria to persist in humans are poorly understood. Group A Streptococcus (GAS) causes the majority of bacterial pharyngitis cases in humans and is prone to persistently inhabit the upper respiratory tract. To gain information about how GAS survives in and infects the oropharynx, we analyzed the transcriptome of a serotype M1 strain grown in saliva. The dynamic pattern of changes in transcripts of genes [spy0874/0875, herein named sptR and sptS (sptR/S), for saliva persistence] encoding a two-component gene regulatory system of unknown function suggested that SptR/S contributed to persistence of GAS in saliva. more...

Organism:

Borreliella burgdorferi; Chlamydia trachomatis; Staphylococcus aureus; Coxiella burnetii; Streptococcus pyogenes; Yersinia pestis; Streptococcus sp. 'group A'

Type:

Expression profiling by array

Platform:

GPL2129

16 Samples

Download data: CEL

(Submitter supplied) We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in the parental serotype M1 GAS isolate MGAS2221 and the parental serotype M49 isolate NZ131

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28036

12 Samples

Download data: XLSX