GEO DataSets

(Submitter supplied) In order to provide global information on gene expression during growth on C2 compounds, microarray analysis of M. extorquens AM1 cells was carried out, comparing ethylamine-grown cells to succinate-grown cells. This comparison has confirmed previous observations on the inducible nature of some of the enzymes involved in C2 metabolism, such as methylamine (and ethylamine) utilization system (mau), putative enzymes for converting acetaldehyde into acetate and acetyl-CoA, and enzymes of the ethylmalonyl-CoA pathway that has been proposed to operate for assimilation of acetyl-CoA into cell biomass.

Organism:

Methylorubrum extorquens; Methylorubrum extorquens AM1

Type:

Expression profiling by array

Platforms:

GPL6262 GPL10058

4 Samples

Download data: TXT

(Submitter supplied) We report RNA-seq datasets profiling the transcriptional response to a sudden change in growth substrate, from succinate to ethylamine. This detailed combined dataset provides a dynamic assessment of the transcriptional response to a metabolic perturbation. These datasets are the first reported RNA-seq datasets for gene expression in Methylobacterium extorquens AM1

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19397

12 Samples

Download data: TXT

(Submitter supplied) In order to provide information about the gene expression response that occurs when cells experience a change in carbon source, succinate limited chemostat cultures of Methylobacterium extorquens AM1 were grown to and maintained at an OD of ~0.63, transferred to flasks and methanol was added. Cells were harvested for RNA extraction at time: 0 min, 10 min, 30 min, 1 hr, 2 hr, 4 hr and 6 hr post transition. more...

Organism:

Methylorubrum extorquens AM1

Type:

Expression profiling by array

Platform:

GPL6262

24 Samples

Download data: TXT, XLS

(Submitter supplied) Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate.

Organism:

Pseudonocardia dioxanivorans CB1190

Type:

Expression profiling by array

Platform:

GPL14784

9 Samples

Download data: CEL

(Submitter supplied) Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 and platform with 250bp paired chemistry and analysed by IsoformSwitchAnalyseR tool of bioconductor Results: Differential transcript expression (DTE) and differential transcript utilization (DTU) of C. glabrata showed that it utilized 292 significant transcripts isoforms during biofilm formation via isoform switching process. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25492

6 Samples

Download data: R, XLSX

(Submitter supplied) The introduction of alternative CO2-fixing pathways such as formate synthesis and assimilation may improve the efficiency of biological carbon fixation that appears to be limited by the enzymatic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we aimed to establish a formate assimilation pathway in the model cyanobacterium Synechocystis sp. PCC 6803. The formate-tetrahydrofolate ligase (FTL) from Methylobacterium extorquens AM1 was expressed in Synechocystis to enable formate assimilation and reduce the loss of fixed carbon in the photorespiratory pathway. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array

Platform:

GPL23938

8 Samples

Download data: TXT

(Submitter supplied) In order for bacteria to thrive, they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorubrum extorquens is an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. more...

Organism:

Methylorubrum extorquens PA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29261

6 Samples

Download data: XLSX