GEO DataSets

(Submitter supplied) Malic enzymes decarboxylate the tricarboxylic acid (TCA) cycle intermediate malate to the glycolytic end-product pyruvate and are well positioned to regulate metabolic flux in central carbon metabolism. The bacterium Sinorhizobium meliloti has a NAD(P)-malic enzyme (DME) and a NADP-malic enzyme (TME) and DME is required for symbiotic N2-fixation. To help understand the role of these enzymes, we examined growth, metabolic and transcriptional consequences resulting from the deletion of these enzymes. more...

Organism:

Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL15586

12 Samples

Download data: PAIR

(Submitter supplied) Symbiotic nitrogen fixation (SNF) is an energetically expensive process performed by bacteria known as rhizobia during endosymbiotic relationships with leguminous plants. The bacteria require the plant to provide a carbon source for generation of the reductant to power SNF. Although it is well known that C4-dicarboxylates (succinate, fumarate, malate) function as the primary, if not sole, carbon source provided to the rhizobia, the relative contribution of each C4-dicarboxylate is not known. more...

Organism:

Pisum sativum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23779

6 Samples

Download data: XLSX

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

Organism:

Sinorhizobium meliloti; Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL10404

36 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P minimizing chemical fertilizers dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti 1021; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti; Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti; Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti; Sinorhizobium meliloti 1021

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti 1021; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. more...

Organism:

Sinorhizobium meliloti 1021; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL10404

6 Samples

Download data: TXT

(Submitter supplied) In metabolically versatile bacteria, carbon catabolite repression (CCR) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rate and fitness. In Pseudomonas putida, the Crc protein and the CrcZ and CrcY small RNAs (sRNAs), which are believed to antagonise Crc, are key players in CCR. Contrary to what occurs in other bacterial species, succinate or glucose elicit a weak CCR in this bacterium. more...

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17091

6 Samples

Download data: TXT

(Submitter supplied) The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria including the rhizobia, Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-seq and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner-Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes. more...

Organism:

Sinorhizobium meliloti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23651

8 Samples

Download data: XLSX

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

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL162 GPL18840

13 Samples

Download data: CEL, WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL18840

4 Samples

Download data: WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides global gene expression analysis was used to determine genes under the regulatory influence of 2 transcription factors: CcmR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides

Type:

Expression profiling by array

Platform:

GPL162

12 Samples

Download data: CEL

(Submitter supplied) Comparison of malic enzyme 3 (ME3) depleted vs non-depleted xenograft tumors. ME3 is an isoform of ME2.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: XLS

(Submitter supplied) We investigated the physiological changes induced by indoleacetic acid (IAA) treatment in the totally sequenced Escherichia coli K-12 MG1655. We used DNA macroarrays to measure the mRNA levels for all the 4,290 E. coli protein-coding genes and observed that 50 genes (1.1 %) exhibited significantly different expression profiles. In particular, genes involved in the tricarboxylic acid cycle (TCA), glyoxylate shunt, and amino acid biosynthesis (leucine, isoleucine, valine and proline) were up-regulated, whereas the fermentative adhE gene was down-regulated. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS2181

Platform:

GPL189

12 Samples

Download data

Analysis of Escherichia coli cells following treatment with indole-3-acetic acid (IAA). IAA is a ubiquitous molecule present in most living organisms and is the main plant growth hormone with auxin activity. Results provide insight into the function of IAA in E. coli.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL189

Series:

GSE4941

12 Samples

Download data

(Submitter supplied) The goal of this study is to compare next-generation sequencing-derived osteoblast transcriptome profilings to identify essential genes during isteoblast differnetiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT

(Submitter supplied) Formyltransferase lacking mutants exhibit reduced growth rates in exponential phase indicating that the function of certain proteins depends on formylated N-termini but it has remained unclear, which cellular processes are abrogated by the lack of formylation. In order to elucidate how global metabolic processes are affected by the absence of formylated proteins the transcription of the fmt mutant was compared with that of the parental strain.

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus RN4220

Type:

Expression profiling by array

Platform:

GPL1339

8 Samples

Download data: CEL

(Submitter supplied) The metabolic changes induced by blocking mitochondrial respiration result in a decrease of 5hmC levels. This experiment aims to further investigate the changes in DNA demethylation induced by Antimycin A treatment using both regular bisulfite- and oxidative bisulfite-chip sequencing.

Organism:

Mus musculus

Type:

Methylation profiling by array

Platform:

GPL31950

12 Samples

Download data: IDAT