GEO DataSets

(Submitter supplied) The level of the Central glycolytic gene regulator (CggR) was engineered in Lactobacillus plantarum NC8 and WCFS1 by over-expression and in-frame mutation of the cggR gene in order to evaluate its regulatory role on the glycolytic gap operon and the glyco

Organism:

Lactiplantibacillus plantarum WCFS1; Lactiplantibacillus plantarum

Type:

Expression profiling by array

Platform:

GPL4318

28 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiles of control Lactobacillus plantarum WCFS1 cells were compared with ctsR, hrcA, and ctsR-hrcA deletion mutants grown in MRS media at 28 and 40 degrees Celcius.

Organism:

Lactiplantibacillus plantarum WCFS1; Lactiplantibacillus plantarum

Type:

Expression profiling by array

Platform:

GPL13984

24 Samples

Download data: TXT

(Submitter supplied) Short-chain fructooligosaccharides (scFOS) and other prebiotics are used to selectively stimulate the growth and activity of lactobacilli and bifidobacteria in the colon. However, there is little information on the mechanisms whereby prebiotics exert their specific effects upon such microorganisms. To study the genomic basis of scFOS metabolism in Lactobacillus plantarum WCFS1, two-colour microarrays were used to screen for differentially expressed genes when grown on scFOS as compared to glucose (not a prebiotic). more...

Organism:

Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL4318

6 Samples

Download data: IMAGENE

(Submitter supplied) In Bacillus cereus the catabolite control protein CcpA was shown to be involved in optimizing the efficiency of glucose catabolism by activating genes encoding glycolytic enzymes including a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase that mediates conversion of D-glyceraldehyde 3-phosphate to 3-phospho-D-glycerate in one single step, and by repressing genes encoding the citric acid cycle and gluconeogenic enzymes. more...

Organism:

Bacillus cereus ATCC 14579

Type:

Expression profiling by array

Platform:

GPL5161

8 Samples

Download data: TXT

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with 1.5 mM gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL15934

3 Samples

Download data: TXT

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL15934

3 Samples

Download data: TXT

(Submitter supplied) Transcriptome profiles of control Lactobacillus plantarum WCFS1 cells were compared with 8% ethanol adapted cells and with 10 min or 30 min 8% ethanol shocked cells.

Organism:

Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL4318

12 Samples

Download data: TXT

(Submitter supplied) In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

9 Samples

Download data: GFF, PAIR

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with resveratrol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a large reshape of nitrogen metabolism whic affects, among others, the pyridine and purine metabolisms as well as the metabolism of aminoacids related to thiol-specific oxidative stress response in this microorganism. more...

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by array

Platform:

GPL22663

3 Samples

Download data: TXT

(Submitter supplied) Background The catabolite control protein A (CcpA) is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in S. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus str. Newman

Type:

Expression profiling by array

Platform:

GPL3931

6 Samples

Download data

(Submitter supplied) Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

9 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

36 Samples

Download data: TXT

(Submitter supplied) The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen. The goal of the study was to use deep sequencing of RNA enriched by co-immunoprecipitation with epitope tagged CsrA to identify CsrA-associated transcripts at the genome level. We found 478 mRNAs or non-coding RNAs to be targets of CsrA. more...

Organism:

Legionella pneumophila str. Paris

Type:

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

Platform:

GPL22984

10 Samples

Download data: WIG

(Submitter supplied) This is a custom commercial array designed by Affymetrix and the Harley McAdams and Lucy Shapiro Labs at Stanford University using the Caulobacter crescentus strain CB15 genome annotation of 2001 (Proc Natl Acad Sci USA. 98:4136-4141). The construction of this Affymetrix GeneChip has been described by McGrath et. al., 2007. Nat Biotechnol. 25:584-592.

Organism:

Caulobacter vibrioides

4 Series

1 Related Platform

18 Samples

Download data: CDF

(Submitter supplied) This is a custom commercial array designed by Affymetrix and the Harley McAdams and Lucy Shapiro Labs at Stanford University using the Caulobacter crescentus strain CB15 genome annotation of 2001 (Proc Natl Acad Sci USA. 98:4136-4141). The construction of this Affymetrix GeneChip has been described by McGrath et. al., 2007. Nat Biotechnol. 25:584-592.

Organism:

Caulobacter vibrioides

4 Series

1 Related Platform

18 Samples

Download data: 1LQ

(Submitter supplied) To characterize regulons of alternative sigma factor SigH, SigL, and SigC in Listeria monocytogenes, in-frame mutant strains were created in the 10403S background. Regulons controlled by these 3 alternative sigma factors were characterized by whole-genome microarrays. The L. monocytogenes 10403S wild type and sigma factor null mutation strains were grown at 37 °C to stationary phase (defined in this study as growth to OD600 = 1.0, followed by incubation for an additional 3 h) prior to RNA isolation. more...

Organism:

Listeria monocytogenes; Listeria innocua

Type:

Expression profiling by array

Platform:

GPL5029

5 Samples

Download data: GPR, TXT

(Submitter supplied) The purpose of this experiment was to examine the differential transcriptional profiles of Caulobacter CB15N grown in M2-Glucose versus M2-Inositol.

Organism:

Caulobacter vibrioides

Type:

Expression profiling by array

Platform:

GPL2749

2 Samples

Download data

(Submitter supplied) A mutant of L. plantarumWCFS1 (deletion of lp_2991) was compared with the wildtype grown in standard MRS broth. Cells were sampled at OD1 for mRNA extraction.

Organism:

Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL9359

2 Samples

Download data: TXT

(Submitter supplied) Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. more...

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL6368

10 Samples

Download data

(Submitter supplied) Wild-type E. coli are prototrophic for all amino acid and nucleotides. These are synthesized by a network of interconnected metabolic pathways from a handful precursors molecules, which are regulated at the level of gene expression. It was hypothesized in this study, that since metabolic pathways are interconnected, transcriptional regulation should be shared across multiple pathways. To uncover these regulatory interactions, cells growing at steady state were perturbed by the addition of an end-metabolite (aa or nt), and were allowed to recover. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3503

22 Samples

Download data: GPR