GEO DataSets

(Submitter supplied) Comprison of the transcriptome of wild type Bacillus subtilis to the mutants sigW, rasP and prsW to select all candidate sigW regulated genes. We identified 89 genes as being sigW regulated, including several non-coding RNA's. The effects of rasP and prsW mutations on sigW regulated genes were relatively mild, implying that RasP or PrsW are not strictly required for sigW activation. The rasP mutant has a peliotropic phenotype, affecting competence development, protein secretion and membrane protein production. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL15150

11 Samples

Download data: PAIR

(Submitter supplied) Abstract of associated manuscript: The Bacillus subtilis extracytoplasmic function (ECF) sigma(M) factor is activated by cell envelope stress elicited by antibiotics, and by acid, heat, ethanol and superoxide stresses. Here, we have used several complementary approaches to identify genes controlled by sigma(M). In many cases, expression is only partially dependent on sigma(M) because of both overlapping promoter recognition with other ECF sigma factors and the presence of additional promoter elements. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL7420

14 Samples

Download data: GPR

(Submitter supplied) Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma factors. Three (sigma M, sigma W and simga X) mediate responses to cell envelope active antibiotics. The functions of sigma Y, sigma Z, sigma V, and YlaC remain largely unknown, and strong inducers of these sigma factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under non-stress conditions between strains carrying deletions in all seven ECF sigma factor genes (Δ7ECF), a sigMWX triple mutant (∆MWX), and the parental 168 strain. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL188

12 Samples

Download data: GPR, TXT

(Submitter supplied) The alternative sigma factor sigmaB has an important role in the acquisition of stress-resistance in many gram-positive bacteria. In the foodborne pathogen Bacillus cereus sigmaB is activated strongly upon a heat shock and other stress conditions. Here we describe the identification of the set of sigmaB-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. more...

Organism:

Bacillus cereus ATCC 14579

Type:

Expression profiling by array

Platform:

GPL4406

7 Samples

Download data

(Submitter supplied) Transcriptional profile of the rpoC G1122D mutant during log growth phase in LB medium.

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL7420

4 Samples

Download data: GPR

(Submitter supplied) To define the ECF sigma sigV - regulated genes during log growth phase in LB media under induction conditions for sigV The seven extracytoplasmic function (ECF) sigma (σ) factors of Bacillus subtilis are broadly implicated in resistance to antibiotics and other cell envelope stressors mediated, in part, by regulation of cell envelope synthesis and modification enzymes. We here define the regulon of σV as including at least 20 operons many of which are also regulated by σM, σX, or σW. more...

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL7420

12 Samples

Download data: GPR

(Submitter supplied) Bacillus subtilis is exposed to a wide range of transitory stress and starvation conditions. Here we investigate the expression changes observed in the B. subtilis wild type strain 168 and its isogenic sigB mutant(BSM29) with respect to each stress condition tested.

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL14719

111 Samples

Download data: TXT

(Submitter supplied) Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an ECF sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

18 Samples

Download data

(Submitter supplied) Whole-genome microarray technology and state-of-the-art proteomic techniques were applied to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic up-shift. This combined experimental approach provided quantitative data for 3961 mRNA profiles, 590 expression profiles of proteins detected in the cytosol and 383 expression profiles of proteins detected in the membrane fraction. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL3502

15 Samples

Download data: CSV

(Submitter supplied) In Gram-positive organisms the general stress response is regulated by the alternative sigma factor sigma B (σB). In C. difficile this sigma factor has been implicated in protection against stressors such as reactive oxygen species and antimicrobial compounds. Here, we show that an anti-σB antibody can be used to demonstrate overexpression of σB in C. difficile and that this overexpression is tolerated for short periods of time, despite its toxicity. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by array

Platform:

GPL25054

16 Samples

Download data: TXT, XLS

(Submitter supplied) Laboratory strains of Bacillus subtilis encodes as many as 16 alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to it being encoded on the large, low copy number plasmid pBS32 that was lost during domestication. more...

Organism:

Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26938

4 Samples

Download data: WIG

(Submitter supplied) The extensively studied intracellular pathogen, L. monocytogenes, is an ideal model for identifying small-molecule agents for treating bacterial infections. By selecting specific biological targets in L. monocytogenes, which are common to Gram-positive pathogens, we could extrapolate drug discovery information derived from this well-studied bacterium. Attenuating the pathogen’s virulence and stress response attributes without killing it, eliminates selective pressure caused by disruption of essential gene functions (as done by current antibiotics) and reduces the likelihood of developing microbes that are impervious to the effects of antibiotics. more...

Organism:

Listeria monocytogenes; Listeria innocua; Listeria monocytogenes 10403S

Type:

Expression profiling by array

Platform:

GPL5029

1 Sample

Download data: GPR

(Submitter supplied) Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13168

6 Samples

Download data: PAIR

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

Organism:

Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL8486 GPL13168

12 Samples

Download data: PAIR

(Submitter supplied) Identification of the specific SigA binding regions on the B. subtilis chromosome during exponential, transition and stationary growth phases. The data served to help the analysis of the repertoire of B. subtilis promoters established from transcriptome profiles.

Organism:

Bacillus subtilis subsp. subtilis str. 168; Bacillus subtilis

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL13168 GPL8486

12 Samples

Download data: PAIR

(Submitter supplied) Genomic DNA prepared from B. subtilis 168 cells grown to stationary phase was hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347).

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Other

Platform:

GPL13168

4 Samples

Download data: PAIR

(Submitter supplied) This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. more...

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL13168

6 Samples

Download data: PAIR

(Submitter supplied) Recent studies revealed the unsuspected complexity of the bacterial transcriptome but its systematic analysis across many diverse conditions remains a challenge. Here we report the condition-dependent transcriptome of the prototype strain B. subtilis 168 across 104 conditions reflecting the bacterium's life-styles. This data set composed of 269 tiling array hybridizations allowed to observe ~85% of the annotated CDSs expressed in the higher 30% in at least one hybridization and thus provide an excellent coverage of the transcriptome of this bacterium. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by genome tiling array

Platform:

GPL13149

269 Samples

Download data: PAIR

(Submitter supplied) Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa.

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL17693

8 Samples

Download data: TXT

(Submitter supplied) We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth on rich medium. DNA microarrays were used to monitor gene transcription in 10-minute intervals at 40 consecutive timepoints. From the growth curve and a PCA analysis of all gene expression levels, we identified 4 distinct growth phases: a lag phase, an exponential growth phase, and very clearly separated early and late stationary growth phases

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL6031

118 Samples

Download data: TXT