GEO DataSets

(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, E. coli BL21 (DE3), P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of different sizes of Polystyrene (PS), including 20 nm, 120 nm and 1 μm. The concentrations were 0.1, 10 mg/L for every size of PS. The group without adding PS was the control group. more...

Organism:

Pseudomonas putida; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24748 GPL18133

28 Samples

Download data: XLSX

(Submitter supplied) P. putida is equipped with functions related to one-carbon (C1) compounds (e.g. methanol, formaldehyde and formate) oxidation—yet pathways to assimilate these carbon sources are largely absent. In this work, we adopted a systems-level approach to study the genetic and molecular basis of C1 metabolism in P. putida (both in EM42 and a double mutant of the characterized formate dehydrogenases in this organism.

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33346

12 Samples

Download data: TXT

(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; Pseudomonas putida KT2440; Pseudomonas protegens CHA0

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) 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 Acinetobacter baylyi ADP1 in response to various antidepressant concentrations for 2 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. more...

Organism:

Pseudomonas putida; Escherichia coli; Acinetobacter baylyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30502

24 Samples

Download data: XLS

(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) Objective: We aimed to decipher how the transcriptome of P.putida would regulate in the presence of 100 mg/L nZVI and its surplus iron released from nZVI, (44.5 μg/L of dissolved iron obtained from nZVI suspension over 24 h in environmental-sourced reservoir) using Next-Seq RAN-sequencing on an Illumina Next-Seq platform Results: Transcriptomic analysis revealed more pronounced differentially expressed genes (DEGs) caused by dissolved iron (3,839 DEGs) against nZVI (945 DEGs). more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22319

18 Samples

Download data: XLSX

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

Organism:

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

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:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

21 Samples

Download data: XLSX

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

Organism:

Pseudomonas putida; Yersinia pseudotuberculosis; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli K-12; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus

Type:

Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms

102 Samples

Download data: GFF

(Submitter supplied) Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. more...

Organism:

Pseudomonas putida

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23992

2 Samples

Download data: GFF

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

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:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26609

15 Samples

Download data: XLSX