GEO DataSets

(Submitter supplied) Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18286 GPL18287

34 Samples

Download data: TXT, XLS

(Submitter supplied) We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18286

47 Samples

Download data: TXT

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

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18286 GPL18287

104 Samples

Download data: TXT

(Submitter supplied) Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including sigma factor-dependent mRNA profiling was performed to define the primary regulon of each sigma factor.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18287 GPL18286

70 Samples

Download data: CSV, PDF, TXT, XLS

(Submitter supplied) We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17739 GPL17738

12 Samples

Download data: TXT

(Submitter supplied) Gene regulation via transcription factors influences the metabolic, adaptive and pathogenic capabilities of the organism. We report the transcriptomes of the mutants of six major P. aeruginosa PA14 trancription factors - RhlR, LasR, Anr, GacA, FleQ and CbrB.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18287 GPL18286

14 Samples

Download data: CSV, PDF, TXT

(Submitter supplied) Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

21 Samples

Download data: TXT, XLSX

(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

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) In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . more...

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23263

28 Samples

Download data: TXT

(Submitter supplied) Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

Organism:

Phikzvirus phiKZ; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28760 GPL23999

44 Samples

Download data: TDF

(Submitter supplied) Bacterial gene expression is controlled by modifying the promoter affinity of the RNA polymerase (RNAP). This control occurs through the substitution of the RNAP σ subunit and by the interaction with transcription factors. The pathogen Pseudomonas aeruginosa contains several σ factors, including σVreI. This protein belongs to the extracytoplasmic function group of the σ70 family. Expression and activity of σECFs are tightly regulated and only occur in response to specific signals. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

2 Samples

Download data: DIFF, TXT, XLS

(Submitter supplied) Background Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps is the initiation of transcription. Identification of the first nucleotide transcribed by the RNA polymerase is therefore essential to understand the underlying regulatory processes, since this provides insight on promoter strength and binding sites for transcriptional regulators, and additionally reveals the exact 5' untranslated region of the transcripts, which often contains elements that regulate translation. more...

Organism:

Staphylococcus epidermidis; Klebsiella aerogenes; Acinetobacter baumannii; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

30 Samples

Download data: TSV

(Submitter supplied) SbrI and SbrR are an extracytoplasmic function sigma factor and its cognate anti-sigma factor, respectively. To identify the SbrIR regulon, we measured gene expression in wild type PAO1 , PAO1 ∆sbrR, and PAO1 ∆sbrIR mutants using microarrays.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL

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

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platforms:

GPL7821 GPL7822

295 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array

Platform:

GPL7822

252 Samples

Download data: GPR