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Links from GEO DataSets

Items: 20

1.

CceR and AkgR regulate of central carbon and energy metabolism in α-Proteobacteria

(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
Series
Accession:
GSE63450
ID:
200063450
2.

Genome-wide protein-DNA interaction analysis of CceR and AkgR transcription factors

(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
Series
Accession:
GSE63449
ID:
200063449
3.

Microarray analysis of Rhodobacter sphaeroides CceR and AkgR deletion strains

(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
Series
Accession:
GSE63448
ID:
200063448
4.

The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides

(Submitter supplied) Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in the facultative photosynthetic bacterium Rhodobacter sphaeroides. We have identified SorY as an sRNA, which is induced under several stress conditions and confers increased resistance against 1O2. SorY by direct interaction decreases the levels of takP mRNA, encoding a TRAP-T transporter. more...
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array
Platform:
GPL15457
2 Samples
Download data: TXT
Series
Accession:
GSE63328
ID:
200063328
5.

R. sphaeroides pRCcsR1-4 vs. R. sphaeroides 2.4.1 pRK415 (aerobic conditions)

(Submitter supplied) Transcriptional profiling of R. sphaeroides pRCcsR1-4 comparing to control R. sphaeroides 2.4.1 pRK415 under aerobic conditions
Organism:
Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array
Platform:
GPL15457
2 Samples
Download data: TXT
Series
Accession:
GSE67145
ID:
200067145
6.

Growth-phase dependent gene regulation in the alpha-proteobacterium Rhodobacter sphaeroides

(Submitter supplied) Global transcriptome analyses at different stages of growth were applied to monitor growth phase-dependent gene expression in the alpha-proteobacterium Rhodobacter sphaeroides. Cultures with low aeration, which underwent strong changes in levels of dissolved oxygen during growth, were compared to aerated cultures, which showed little variation in levels of dissolved oxygen. Cells were in stationary phase for 12 h or for 57 h before dilution into fresh medium. more...
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17213
8 Samples
Download data: WIG
Series
Accession:
GSE71844
ID:
200071844
7.

Comparative transcriptome analysis of a novel obligate Methylomonas sp. DH-1 reveals key differences in the transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol

(Submitter supplied) We integrated genomic and transcriptomic analysis of a newly isolated obligate Methylomonas sp. DH-1 grown on methane and methanol. Comparative transcriptomic analysis between methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, the secondary metabolites pathways and the oxidative stress related genes
Organism:
Methylomonas sp. DH-1
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23786
6 Samples
Download data: TXT
Series
Accession:
GSE101494
ID:
200101494
8.

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks

(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:
GPL162 GPL18842 GPL17213
15 Samples
Download data: CEL, WIG
Series
Accession:
GSE58658
ID:
200058658
9.

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [ChIP-Seq]

(Submitter supplied) By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341).
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17213 GPL18842
4 Samples
Download data: WIG
Series
Accession:
GSE58648
ID:
200058648
10.

An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [Affymetrix]

(Submitter supplied) Rhodobacter sphaeroides is the best studied photosynthetic bacterium, yet much remains unknown about its transcriptional regulatory processes on a genome-scale. We developed a work-flow for genome-scale reconstruction of transcriptional regulatory networks and applied it to sequence and gene expression data sets available for R. sphaeroides. To assess the predictive performance of our reconstructed model, we generated global transcript level and/or protein-DNA interaction data for 3 transcription factors (PpsR, RSP_0489 and RSP_3341). more...
Organism:
Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides
Type:
Expression profiling by array
Platform:
GPL162
11 Samples
Download data: CEL, TXT
Series
Accession:
GSE58553
ID:
200058553
11.

FnrL regulon in Rhodobacter sphaeroides

(Submitter supplied) In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity.
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10463
9 Samples
Download data: GFF, PAIR
Series
Accession:
GSE22027
ID:
200022027
12.

Metabolic imbalance caused by loss of malic enzymes in the legume endosymbiont Sinorhizobium meliloti

(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
Series
Accession:
GSE71308
ID:
200071308
13.

Global analysis of photosynthesis transcriptional regulatory networks

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18840 GPL162 GPL18841
32 Samples
Download data: CEL, WIG
Series
Accession:
GSE58717
ID:
200058717
14.

Global analysis of photosynthesis transcriptional regulatory networks [ChIP-seq]

(Submitter supplied) To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.
Organism:
Cereibacter sphaeroides
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18841 GPL18840
12 Samples
Download data: WIG
Series
Accession:
GSE58716
ID:
200058716
15.

Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling]

(Submitter supplied) To gain a deeper understanding of the transcription factors that regulate photosynthesis in Rhodobacter sphaeroides global gene expression analysis was used to determine the expression profiles of the deletion mutants of 4 transcription factors (FnrL, PrrA, CrpK and RSP_2888) known or predicted to be involved in the regulation of photosynthesis.
Organism:
Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array
Platform:
GPL162
20 Samples
Download data: CEL, TXT
Series
Accession:
GSE58554
ID:
200058554
16.

A key regulator of the glycolytic and gluconeogenic central metabolic pathways in Sinorhizobium meliloti

(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
Series
Accession:
GSE100765
ID:
200100765
17.

Expression analysis of Magnetospirillum magneticum AMB-1 WT, ΔMAI, ΔctrA, ΔdivK, and ΔctrA complemented with CtrA D51E, CtrA D51A, and an empty vector control

(Submitter supplied) Investigation of whole genome expression changes in Magnetospririllum magneticum mutants, probing the role of the CtrA regulatory pathway. The mutants are further described in a manuscript submitted for publication at J. Bacteriology. Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and post-translational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. more...
Organism:
Paramagnetospirillum magneticum AMB-1
Type:
Expression profiling by array
Platform:
GPL15199
16 Samples
Download data: PAIR
Series
Accession:
GSE35625
ID:
200035625
18.

Global control of carbon flux in Bifidobacterium breve UCC2003

(Submitter supplied) In this paper, two predicted lac I type transcription factors (TFs) were characterised and shown to be involved in the regulation of the central metabolic pathways of B. breve UCC2003. Although, genetically different, these TF were functionally very similar. When first identified these TFs were named AraQ and MalR1, due to their predicted associations with arabinose and maltose metabolism, respectively. more...
Organism:
Bifidobacterium breve UCC2003
Type:
Expression profiling by array
Platform:
GPL13210
4 Samples
Download data: TXT
Series
Accession:
GSE108949
ID:
200108949
19.

The NtrYX two-component system regulates the bacterial cell envelope

(Submitter supplied) To investigate the R. sphaeroides NtrYX two component system on RNA transcript levels, we used global RNA sequencing (RNA-seq) to compare transcript abundance in parent and DntrYX strains grown under aerobic conditions. Our previous studies were performed in strains deficient at synthesizing the polyhydroxybutyrate, so we used strains D0382 and DNtrYXD0382, herein referred to as parent and DntrYX, respectively. more...
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18842 GPL28141
11 Samples
Download data: WIG, XLSX
Series
Accession:
GSE145442
ID:
200145442
20.

GlpR functions as a global DeoR-type regulator of metabolic gene transcription in the haloarchaeon Haloferax volcanii

(Submitter supplied) Investigation of gene expression in ∆glpR mutant strains vs wild type in response to glycerol and glucose.
Organism:
Haloferax volcanii
Type:
Expression profiling by array
Platform:
GPL21414
12 Samples
Download data: PAIR
Series
Accession:
GSE77589
ID:
200077589
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