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Links from GEO DataSets

Items: 20

1.

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
2.

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
3.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulphur metabolism and represents a new type of iron-sulphur binding protein

(Submitter supplied) Iron-sulphur (Fe-S) clusters are ensembles of iron and sulphide centres. They are found in all life forms and are important components of many enzymes involved in diverse cellular processes, including respiration, DNA synthesis or gene regulation. However, the increase in oxygen after the emergence of oxygenic photosynthesis created a threat to Fe–S proteins and, consequently, to the organisms relying on them. more...
Organism:
Cereibacter sphaeroides 2.4.1
Type:
Expression profiling by array
Platform:
GPL15457
2 Samples
Download data: TXT
Series
Accession:
GSE65537
ID:
200065537
12.

Regulation of hydrogen peroxide-dependent gene expression in Rhodobacter sphaeroides: Regulatory functions of OxyR

(Submitter supplied) Transcriptome profiling of Rhodobacter sphaeroides cells (WT and delta-oxyR mutant) grown in semiaerobic conditions, 7 and 30 min after addition of H2O2 up to 1 mM Keywords: time series
Organism:
Cereibacter sphaeroides 2.4.1; Cereibacter sphaeroides
Type:
Expression profiling by array
Dataset:
GDS1908
Platform:
GPL162
15 Samples
Download data
Series
Accession:
GSE2829
ID:
200002829
13.
Full record GDS1908

Hydrogen peroxide response: time course

Expression profiling of oxyR deletion mutant and wild type cells following treatment with 1 mM hydrogen peroxide. OxyR is a transcription factor that senses oxidative stress. Results provide insight into the mechanisms involved in oxidative stress tolerance.
Organism:
Rhodobacter sphaeroides; Rhodobacter sphaeroides 2.4.1
Type:
Expression profiling by array, count, 2 genotype/variation, 3 time sets
Platform:
GPL162
Series:
GSE2829
15 Samples
Download data
14.

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
15.

An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network.

(Submitter supplied) Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism-environment interactions, and difficulty of estimating the activity of regulatory factors. more...
Organism:
Bacillus subtilis
Type:
Expression profiling by array
Platform:
GPL15179
268 Samples
Download data: TXT
Series
Accession:
GSE67023
ID:
200067023
16.

S. coelicolor M145 SMM medium time course study

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Streptomyces coelicolor
Type:
Expression profiling by array
Platform:
GPL4908
43 Samples
Download data: GPR, TXT
Series
Accession:
GSE22399
ID:
200022399
17.

S. coelicolor M752 SMM medium time course study

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. more...
Organism:
Streptomyces coelicolor
Type:
Expression profiling by array
Platform:
GPL4908
9 Samples
Download data: GPR, TXT
Series
Accession:
GSE22398
ID:
200022398
18.

S. coelicolor M145 SMM medium time course study (Culture # 3)

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.
Organism:
Streptomyces coelicolor
Type:
Expression profiling by array
Platform:
GPL4908
15 Samples
Download data: TXT
Series
Accession:
GSE22397
ID:
200022397
19.

S. coelicolor M145 SMM medium time course study (Culture # 2)

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.
Organism:
Streptomyces coelicolor
Type:
Expression profiling by array
Platform:
GPL4908
8 Samples
Download data: TXT
Series
Accession:
GSE22395
ID:
200022395
20.

S. coelicolor M145 SMM medium time course study (Culture # 1)

(Submitter supplied) Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants.
Organism:
Streptomyces coelicolor
Type:
Expression profiling by array
Platform:
GPL4908
20 Samples
Download data: GPR, TXT
Series
Accession:
GSE22394
ID:
200022394
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