GEO DataSets

(Submitter supplied) During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21373 GPL24109 GPL18561

107 Samples

Download data: WIG

(Submitter supplied) The B. subtilis transcriptome was analyzed under conditions of different growth rates, i.e. during growth in different cultivation media. Gene-level intensities were scaled based on the intensity values of 10 spike-in transcripts. This approach allowed to determine the total mRNA fraction out of the total RNA pool. The data revealed that the proportion of total mRNA in total RNA remained constant across samples which implies that total mRNA abundance in B. more...

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL10901

16 Samples

Download data: TXT

(Submitter supplied) The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Wild-type strain and spx mutant cells exposed or not to diamide stress were subjected to tiling array gene expression analysis. more...

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8486

4 Samples

Download data: PAIR

(Submitter supplied) Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL14548

30 Samples

Download data: BEDGRAPH

(Submitter supplied) In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome.

Organism:

Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL21981

12 Samples

Download data: TXT

(Submitter supplied) In this work we conducted RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this data we analysed the transcriptome-wide effects of NusA on RNA polymerase pausing and found that NusA has modest pause stimulating as well as suppressing effects throughout the genome.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18561

8 Samples

Download data: BW

(Submitter supplied) In this work we conducted Term-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this approach, we found that NusG is an intrinsic termination factor that works single and cooperatively with NusA.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24109

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19910

12 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Genome-wide comparative transcriptome analysis of the Bacillus subtilis parent strain PY79 and its yvfI derivative with yvfI::T10::spc (TEK1) grown in PA medium Detailed description of sample preparation and microarray conditions can be also found in Irigul et al to be submitted

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL6031

3 Samples

Download data: TXT

(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; Bacillus subtilis subsp. subtilis str. 168

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; Bacillus subtilis subsp. subtilis str. 168

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) Identification of the specific WalR (YycF) binding regions on the B. subtilis chromosome during exponential and phosphate starvation growth phases. The data serves to extend the WalRK regulon in Bacillus subtilis and its role in cell wall metabolism, as well as implying a role in several other cellular processes.

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13168

12 Samples

Download data: PAIR, TXT