GEO DataSets

(Submitter supplied) Mature tRNA pools were measured using an adaptation of Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq) (Shigematsu et al., 2017) in nine strains derived from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing the single-copy serCGA gene by genetic engineering, and (ii) duplicating the serTGA gene during a subsequent, compensatory evolution experiment. more...

Organism:

Pseudomonas fluorescens

Type:

Other

Platform:

GPL28120

27 Samples

Download data: XLSX

(Submitter supplied) Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in eight strains dervied from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing multi-copy tRNA genes by genetic engineering, and (ii) duplicating tRNA genes during a subsequent, compensatory evolution experiment. more...

Organism:

Pseudomonas fluorescens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL28120

24 Samples

Download data: XLSX

(Submitter supplied) HutC in Pseudomonas is a representative member of the HutC/GntR family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate binding domain. HutC is generally known to represses expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28231

2 Samples

Download data: CSV

(Submitter supplied) To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). more...

Organism:

Pseudomonas fluorescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24598

2 Samples

Download data: XLS

(Submitter supplied) We report mRNA expression data from Pseudomonas fluorescens SBW25 wild type and two evolved strains (Beaumont et al., 2009). The evolution of one of these strains saw the emergence of colony switching; 1B4 switches rapidly between two different colony phenotypes. These two phenotypes were found to be genetically identical. Thus, in order to gain insight into epigenetic mechanisms of switching, we were interested in identifiying gene expression differences between ancestors and the 1B4 colony phenotypes.

Organism:

Pseudomonas [fluorescens] SBW25

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17454

4 Samples

Download data: TXT, XLSX