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Expression data from Pseudomonas putida KT2440 (Progenika oligo array data)

ABSTRACT: We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C

ORGANISM(S): Pseudomonas putida KT2440

PROVIDER: GSE24174 | GEO | 2011/03/25

SECONDARY ACCESSION(S): PRJNA133711

REPOSITORIES: GEO

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Expression data from Pseudomonas putida KT2440 (Affymetrix data)

Project description:We used Affymetrix microarrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C

2011-03-25 | GSE24173 | GEO

Expression data from Pseudomonas putida KT2440 (RNA-Seq data)

2011-02-01 | GSE24175 | GEO

Expression data from Pseudomonas putida KT2440 (Progenika oligo array data)

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C Culture was grown in minimal medium supplemented with succinate at 30°C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10°C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction. Data from four replicate hybridizations (two dye-swaps) were combined into a single ratio value. Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file available on the Series record.

2011-03-24 | E-GEOD-24174 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440 (Affymetrix data)

Project description:We used Affymetrix microarrays to monitore the gene expression of P. putida after a cold shock from 30°C to 10°C Culture was grown in minimal medium supplemented with succinate at 30°C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10°C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.

2011-03-24 | E-GEOD-24173 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440 Tn5 mutants

Project description:We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30°C to 10°C. The 10°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044).

2014-02-01 | GSE28257 | GEO

Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments.

2014-02-01 | GSE26785 | GEO

Expression data from Pseudomonas putida KT2440 (RNA-Seq data)

Project description:We used cDNA generated from total mRNA for RNA-Seq analysis (Genome Analyzer II at GATC Biotech AG) to monitore the gene expression of P. putida after a cold shock from 30M-BM-0C to 10M-BM-0C Culture was grown in minimal medium supplemented with succinate at 30M-BM-0C. In mid-exp. phase cells were harvested for subsequent RNA extraction (standard condition) and medium was cooled down to 10M-BM-0C. Two hrs after reaching the temperature, cells were again harvested for RNA extraction.

2011-02-01 | E-GEOD-24175 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440 Tn5 mutants

Project description:We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30Â°C to 10Â°C. The 10Â°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044). Cultures were grown in minimal medium supplemented with succinate at 30Â°C. In mid-exponential phase, cells were cooled down to 10Â°C. Two hours after the medium had reached 10Â°C, cells were harvested for subsequent RNA extraction.

2014-02-01 | E-GEOD-28257 | biostudies-arrayexpress

Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments. After ensuring steady state conditions on benzoate, the stimuli were introduced by changing the carbon source from benzoate to glucose, from glucose to fructose and from fructose to benzoate, respectively. The single stimuli were monitored over a time period from 10 to 120 minutes after changing the carbon source by three representative timepoints. Moreover, the steady state conditions were compared among each other. Supplementary file: Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file.

2014-02-01 | E-GEOD-26785 | biostudies-arrayexpress

The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

Project description:Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose.

2013-07-23 | GSE46491 | GEO

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