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:

Escherichia coli; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18133 GPL24748

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 KT2440; Pseudomonas protegens CHA0; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28971 GPL29079 GPL32953

22 Samples

Download data: 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 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:

Escherichia coli; Acinetobacter baylyi; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30502

24 Samples

Download data: XLS

(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) 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) creatine regulon is small and electrophoretic mobility shift demonstrates specific CahR binding only at the creA promoter suggesting much of the regulon is due to induction by downstream products. This study identifies ligand specificity and provides biological function to a previously uncharacterized GATR, contributing to our understanding of bacterial organic nitrogen compound metabolism.

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28851

12 Samples

Download data: CSV

(Submitter supplied) We identified binding sites genome-wide for carbon metabolism transcriptional response regulators in Pseudomonas stutzeri RCH2, Pseudomonas putida KT2240, Pseudomonas fluorescens FW300-N2E2 and FW300-N2C3 by DNA-affinity-purified (DAP) sequencing.

Organism:

Stutzerimonas stutzeri; Pseudomonas fluorescens; Pseudomonas putida

Type:

Other

Platforms:

GPL29080 GPL29079 GPL29078

96 Samples

Download data: WIG

(Submitter supplied) Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences that are bound in vivo by Rsm proteins, in order to identify potential regulatory targets for each of them. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to identify 709 targets, 75 of them common to the three proteins. more...

Organism:

Pseudomonas putida

Type:

Other

Platform:

GPL28851

14 Samples

Download data: WIG, XLSX

(Submitter supplied) ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

Organism:

Pseudomonas protegens; Pseudomonas chlororaphis; Pseudomonas aeruginosa; Pseudomonas putida

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas putida is a microorganism with great potential for industry due to its stress-endurance traits and easy manipulation of the metabolism. However, optimization is still required to improve production yields. In the last years, manipulation of bacterial small non-coding RNAs (ncRNAs) has been recognized as an effective tool to improve the production of industrial compounds. So far, very few ncRNAs are annotated in P. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26512

36 Samples

Download data: TXT

(Submitter supplied) Metabolically versatile bacteria use catabolite repression control to select their preferred carbon sources, thus optimizing carbon metabolism. In pseudomonads, this occurs through the combined action of the proteins Hfq and Crc, which form stable tripartite complexes at target mRNAs, inhibiting their translation. The activity of Hfq/Crc is antagonised by small RNAs of the CrcZ family, the amounts of which vary according to carbon availability. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19659

4 Samples

Download data: TXT

(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 antiepileptic drug carbamazepine. Three concentrations of carbamazepine were applied, which were 0.05 mg/L, 10.0 mg/L and 50.0 mg/L (refer to low, medium and high, respectively). The group without dosing carbamazepine was the control group. more...

Organism:

Escherichia coli; Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24748

12 Samples

Download data: TXT

(Submitter supplied) We constructed fleQ mutant strain and analyzed its regulation role through gene expression profile compared to the wild-type KT2442.

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23992

3 Samples

Download data: XLSX

(Submitter supplied) We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E and E. coli growing in co-cultures

Organism:

Pseudomonas putida; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23101 GPL19659 GPL14548

6 Samples

Download data: XLSX

(Submitter supplied) The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22319

12 Samples

Download data: TXT, XLSX

(Submitter supplied) The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19659

18 Samples

Download data: XLSX

(Submitter supplied) In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplex structures have been implicated in post-transcriptional gene regulation and diseases, direct evidence for quadruplex formation in cells has been lacking. Here, we developed a suite of methods that identify RNAs with quadruplex-forming ability and measure their folding state in living cells. more...

Organism:

Mus musculus; Parasynechococcus marenigrum WH 8102; Pseudomonas putida; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli

Type:

Other

6 related Platforms

35 Samples

Download data: TXT

(Submitter supplied) Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20783

2 Samples

Download data: TXT

(Submitter supplied) Transcriptomics analysis of biopolymer (medium chain length polyhydroxyalkanoate) producing strain P.putida LS46 cultured with biodiesel derived waste carbon sources: studies of cellular adaptation to the industrial waste streams and metabolic profiling under the polymer producing conditions. We are reporting RNAseq analysis data here as part of our multi-level Omics study of medium chain length polyhydroxyalkanoate (mcl-PHA) producing strain P.putida LS46 culture with biodiesel derived waste glycerol and waste fatty acids. more...

Organism:

Pseudomonas putida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19659

8 Samples

Download data: TXT