GEO DataSets

(Submitter supplied) To get insights in the electrogenic anaerobic lifestyle of P. putida KT2440 cultivated in a bioelectrochemical system (BES), we employed whole genome microarray expression profile.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL31933

12 Samples

Download data: TXT, XLSX

(Submitter supplied) KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. more...

Organism:

Pseudomonas putida KT2440; Pseudomonas protegens CHA0; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29079 GPL28971 GPL32953

22 Samples

Download data: TXT

(Submitter supplied) The bacterium Pseudomonas putida KT2440 has the ability to reduce selenite forming nanoparticles of elemental selenium. This is the transcriptome of the organism when cultured in the presence of selenite.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

4 Samples

Download data: CSV

(Submitter supplied) In an evolutionary experiment on high hemin concentrations, a frameshift mutation in the ChrS gene was figured out to be striking in survival at high hemin concentrations (Ala245fs). Apart from high upregulation of heme exporter hrtB, microarrays should reveal further different controlled genes compared to the WT.

Organism:

Corynebacterium glutamicum; Bacillus subtilis subsp. subtilis str. 168; Gluconobacter oxydans 621H; Escherichia coli str. K-12 substr. MG1655; Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL32387

3 Samples

Download data: GPR

(Submitter supplied) mRNA was sampled during exponential growth (OD600 = 2, Control), then an inhibitory dose of 5 mM catechol was added to the culture and samples were taken again after 1h (Stress)

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL31933

6 Samples

Download data: CSV, TXT

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of CuO NPs and Cu2+. The concentrations were 5 μmol/L for CuO NPs and Cu2+. The group without dosing CuO NPs or Cu2+ was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these CuO NPs and Cu2+ on transcriptional levels can be revealed. more...

Organism:

Pseudomonas putida KT2440; Plasmid RP4; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

9 Samples

Download data: XLSX

(Submitter supplied) This dataset is a part of putidaPRECISE321, which was utilized to unveil the trnascriptional regulatory network of Pseudomonas putida KT244. Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28478

81 Samples

Download data: CSV

(Submitter supplied) Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida, an important organism for bioproduction. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28478 GPL28971

22 Samples

Download data: CSV

(Submitter supplied) Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously engineered to produce muconate from glucose; however, periplasmic oxidation of glucose causes substantial 2-ketogluconate accumulation, reducing product yield and selectivity. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28478

9 Samples

Download data: CSV

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

Organism:

Pseudomonas putida KT2440; Plasmid RP4; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

30 Samples

Download data

(Submitter supplied) The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of six non-antibiotic pharmaceuticals, including ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and iopromide. The concentrations were 0.5 mg/L for ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and 1.0 mg/L for iopromide. more...

Organism:

Pseudomonas putida KT2440; Plasmid RP4; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

21 Samples

Download data: XLSX

(Submitter supplied) Efficient utilization of lignocellulosic biomass-derived sugars is essential to improve the economics of biorefinery. While Pseudomonas putida is a promising microbial host, its usage is limited because this strain cannot utilize xylose or galactose as a sole carbon source. To address this issue, we heterologously introduced a xylose utilizing gene (xylD) from Caulobacter crescentus and a galactose operon (galETKM) from E. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28971

14 Samples

Download data: CSV

(Submitter supplied) Investigation of the impact of an overexpression of cg1978 on gene expression under standard conditions (CGXII-Glucose)

Organism:

Gluconobacter oxydans; Pseudomonas putida KT2440; Escherichia coli; Corynebacterium glutamicum; Corynebacterium glutamicum ATCC 13032; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL26911

3 Samples

Download data: GPR

(Submitter supplied) The entire set of flagellar structural components and flagellar-specific transcriptional regulators, as well as much of the core chemotaxis machinery, is encoded into a >70 kbp cluster in Pseudomonas putida KT2440 genome. We have performed RNA-seq of the wild-type strain in order to identify operon boundaries and promoters location in this cluster.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28478

3 Samples

Download data: TXT

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. more...

Organism:

Plasmid RP4; Escherichia coli K-12; Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

15 Samples

Download data: XLSX

(Submitter supplied) We report the transcriptomic profiles of 2 different Pseudomonas putida derivatives when they are grown in MME medium supplemented with either ammonium or nitrate as the sole nitrogen source. Expression of both heterologous and native genes are examined.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25301

14 Samples

Download data: CSV

(Submitter supplied) DNA microarray analysis was performed to check whether the addition and/or oxidation of L-arabinose to the growth medium of G.oxydans 621H possibly affects short-term global gene expression.

Organism:

Escherichia coli; Corynebacterium glutamicum; Bacillus subtilis subsp. subtilis str. 168; Gluconobacter oxydans 621H; Gluconobacter oxydans; Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL28615

1 Sample

Download data: GPR

(Submitter supplied) Transcriptome of the wildtype or evolved Pseudomonas putida KT2440

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28478

16 Samples

Download data: CSV

(Submitter supplied) P. putida KT2440 was mixed in a conjugation filter with either E. coli BW27783-NxR bearing no plasmid (NP), E. coli BW27783-NxR bearing pSU2007 (ardC+) or E. coli BW27783-NxR bearing pLGM25 (ardC-). RNA-seq results showed that: (a) R388 genes involved in conjugation are highly upregulated in the ardC+ condition with respect to the ardC- condition. (b) a number of donor E. coli genes and pathways involved in flagellar motility, SOS and stress responses and different metabolic pathways are downregulated in the ardC- condition with respect to NP or ardC+ conditions. more...

Organism:

Escherichia coli; Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28297

3 Samples

Download data: TXT

(Submitter supplied) We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL28267

16 Samples

Download data: CALLS, PAIR, TXT