GEO DataSets

(Submitter supplied) Halobacterium salinarum ∆cspD1 transcription factor deletion mutant and control strain NRC-1 of Halobacterium salinarum were grown to mid-logarithmic phase in batch mode in a New Brunswick BioFlo100 modular bench top fermentor (New Brunswick Scientific) in CM medium as described in (Schmid et al., 2007, Genome Res, 17(10):1399-413. At mid-log phase, oxygen sparging and agitation were stopped to induce anoxia. more...

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL22925

6 Samples

Download data: CSV

(Submitter supplied) Previous work identified the winged helix-turn-helix DNA binding transcription factor (TF) RosR (encoded by VNG0258H gene), which dynamically regulates expression of more than 300 genes in response to oxidative stress in Halobacterium salinarum (Sharma 2012). RosR is required for survival of oxidants from multiple sources (e.g. H2O2 and paraquat), as deletion mutants are impaired for ROS outgrowth. Genes directly and indirectly controlled by RosR in response to ROS encode macromolecular repair functions. In the current study, we ask which of these genes are direct targets of RosR regulation. Dynamic chromatin immunoprecipitation combined with microarray (ChIP-chip) analysis validates that genes encoding these functions are direct targets of RosR binding and control. In addition, new RosR direct target genes are identified, including those encoding central cellular functions and a surprisingly high number of other TFs. The majority of the 252 sites throughout the genome are RosR-bound in the absence of stress and cleared of RosR binding in the presence of H2O2. However, binding is dynamic, with promoter-specific differences in the timing of RosR-DNA release and re-binding relative to ROS exposure.

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL18848

20 Samples

Download data: TXT

(Submitter supplied) Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. more...

Organism:

Haloferax volcanii DS2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30888

8 Samples

Download data: WIG

(Submitter supplied) We report high-throughput RNA sequencing of WT, ΔfnrΔarcA (FA), ΔfnrΔihf (FI) and ΔarcAΔihf (AI) strains in the exponential phase under anaerobic fermentative conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24659

8 Samples

Download data: TXT

(Submitter supplied) Arabidopsis plants grown in a hydroponic media with sufficient Nitrogen were given a 60mM supply of Nitrogen. Triplicate sets of plants were sampled at time points 0,5,10,15,20,30,45,60,90 and 120 minutes after supply from treated and control plants (20mM KCl). The samples were flash frozen in liquid N and used to construct RNA-Seq libraries to assay transcriptional changes in the shoots and roots, separately, in response to Nitrogen.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

114 Samples

Download data: TXT

(Submitter supplied) Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV and gamma radiation. Genome-wide dynamics alteration of gene the GRN has been implicated in such resistance. However, the molecular function of transcription regulatory proteins involved in this response remains unknown. Here we have leveraged several existing GRN and systems biology datasets for H. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

150 Samples

Download data: TXT

(Submitter supplied) The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media and after 10 days protoplasts were generated from root tissue, Cells were transfected with a vector containing the GR-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

56 Samples

Download data: CSV

(Submitter supplied) We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

12 Samples

Download data: TXT

(Submitter supplied) Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24129

51 Samples

Download data: TXT

(Submitter supplied) Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. more...

Organism:

Candida albicans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24129

12 Samples

Download data: BW

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

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platform:

GPL23999

40 Samples

Download data

(Submitter supplied) Determination of the binding sites of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23999

24 Samples

Download data: XLSX

(Submitter supplied) Determination of the impact of the individual deletion of 7 transcription factors (PA0535, PA1359, PA1884, PA2312, PA4499 (PsdR), PA4987 and PA5301 (PauR)) in Pseudomonas aeruginosa PAO1.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23999

16 Samples

Download data: XLSX

(Submitter supplied) Previous work characterized TrmB as a global glucose responsive metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ~100 metabolic enzyme-coding genes. Using a dynamic perturbation approach, we elucidate the topology of the metabolic GRN in Halobacterium salinarum. We assayed gene expression in a wild-type and trmB knockout strain before and immedeatly following glucose perturbation. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Other

Platform:

GPL17188

48 Samples

Download data: XLS

(Submitter supplied) The basidiomycetous fungus Cryptococcus has been known as radiation resistant fungi and is found in highly radioactive environments such as the damaged nuclear reactor at Chernobyl. Although Cryptococcus exhibits greater resistant for gamma radiation than the model yeast Saccharomyces cerevisiae, the resistant mechanism of gamma radiation remains elusive. To elucidate a unique regulatory system for radiation-resistance in C. more...

Organism:

Cryptococcus neoformans; Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by array

Platform:

GPL18333

12 Samples

Download data: GPR

(Submitter supplied) Addition of 3 new arrays made from carbon limited chemostat of CENPK113-7D and 3 new arrays made from aerobic carbon limited chemostat of CENPK113-7D Complmentary data to the data of the serie GSE1723. Keywords: Chemostat-based transcriptome response comparison

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

30 Samples

Download data: CEL, EXP

(Submitter supplied) The goal of this study was to study this interaction by analyzing genome-wide transcriptional responses to four different nutrient-limitation regimes under aerobic and anaerobic conditions in chemostat cultures of S. cerevisiae. This ‘two-dimensional’ approach resulted in a new, robust set of ‘anaerobic’ and ‘aerobic’ signature transcripts for S. cerevisiae, as well as to a refinement of previous reports on nutrient-responsive genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS777

Platform:

GPL90

24 Samples

Download data: CEL, EXP

Expression profiling of MATa CEN.PK113-7D chemostat cultures grown either aerobically or anaerobically in media limited for either glucose, nitrogen, phosphorous, or sulfur. Results provide insight into the interaction between oxygen and nutrient responsive pathways.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 4 growth protocol, 2 stress sets

Platform:

GPL90

Series:

GSE1723

24 Samples

Download data: CEL, EXP

(Submitter supplied) The interaction between soybean and its destructive insect (cotton worm) is complicated. In this paper, the timecourse of induced responses to cotton worm were characterized in two soybean lines, suggesting complex results with different timepoints of peak induced resistance in resistant (WX) and susceptible (NN) soybean lines. To get a better understanding of induced resistant mechanisms of soybean against herbivory, two sets of transcriptome profiles of WX and NN at their peak induced resistant timepoints were compared by microarrays

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

12 Samples

Download data: CEL

(Submitter supplied) Regulation of gene expression in biological systems is a complex, nonlinear process composed of context specific interactions, from signaling and transcription to genome modification. Modeling gene regulatory networks (GRNs) can be limited due to a lack of direct measurements of regulatory features in genome-wide screens. Most GRN inference methods are consequently forced to model covariance between regulatory genes and their targets as a proxy for causal interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

3 Samples

Download data: TSV