GEO DataSets

(Submitter supplied) Investigating the possible physiological role of CYP174A1 (cyc) in H. salinarum

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL15637

2 Samples

Download data: TXT

(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) RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23553

6 Samples

Download data: TXT

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

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL17005 GPL13426

58 Samples

Download data: TXT

(Submitter supplied) Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1.

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13426

34 Samples

Download data: TXT

(Submitter supplied) We validated context dependent regulation by two FFRPs AsnC and VNG1237C by deleting the FFRP and testing the effect on downstream target genes. For validtion of AsnC condition specific regulation we grew wild-type and delta-AsnC in the presence of 4mM paraquat (PQ) and samples at 1 and 160 minutes post addition of this sub-lethal dose of PQ. For validation of VNG1237C we grew wild-type and delta-VNG1237C in a standard growth curve sampling at OD 0.18 and 1.15.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL17005

24 Samples

Download data: TXT

(Submitter supplied) To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

8 Samples

Download data: TXT

(Submitter supplied) Halobacterium salinarum is an extreme halophilic archaeon adapted to total salinities upwards of 4 M. Here we studied gene expression in H. salinarum grown in ten ion composition media that vary in two major aspects of ion composition: [NaCl] and Mg:K ratio.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

20 Samples

Download data: TXT

(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 microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others’ fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD) on a population’s growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13682

32 Samples

Download data: CSV, TXT

(Submitter supplied) As part of a comprehensive post-genomic investigation of the model archaeon Halobacterium sp. NRC-1, we used whole genome DNA microarrays to compare transcriptional profiles of cells grown anaerobically via arginine fermentation versus cells either respiring aerobically in the presence of oxygen or anaerobically using trimethylamine N-oxide (TMAO) as a terminal electron acceptor.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL15637

5 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) Halobacterium salinarum is a halophillic archea that is capable of sustaining growth despite dramatic changes to the concentration of ions in its extracellular environment. Here we studied H. salinarum's specific adaptation response to the transition metal copper.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13682

49 Samples

Download data: CSV

(Submitter supplied) Numerous lineage-specific expansions of the transcription factor B (TFB) family in archaea suggests an important role for expanded TFBs in encoding environment-specific gene regulatory programs. Given the characteristics of hypersaline lakes the unusually large numbers of TFBs in halophilic archaea further suggests that they might be especially important in rapid adaptation to the challenges of a dynamically changing environment. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13426

28 Samples

Download data: TXT

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

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL13683 GPL13682

61 Samples

Download data: CSV

(Submitter supplied) Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well understood in organisms that dwell in environments at the extremes of pH, temperature, and salinity. Under conditions of limited iron, the extremophile Halobacterium salinarum, a salt-loving archaeon, mounts a specific response to scavenge iron for growth. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13683

13 Samples

Download data: CSV

(Submitter supplied) Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well understood in organisms that dwell in environments at the extremes of pH, temperature, and salinity. Under conditions of limited iron, the extremophile Halobacterium salinarum, a salt-loving archaeon, mounts a specific response to scavenge iron for growth. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13682

48 Samples

Download data: CSV, TXT

(Submitter supplied) Oxidative stress (OS) results from genetic defects or stressful environmental challenges that cause unchecked production of reactive oxygen species (ROS). OS has been implicated in many diseases due to its wide ranging damage to nucleic acids, proteins and lipids. Using Halobacterium salinarum NRC-1, an extremophile that thrives under conditions of excessive OS, we have constructed a systems model for oxidative stress response (OSR) by integrating transcriptional changes induced by treatments with H2O2 and paraquat, functional associations inferred through comparative genomics, and de novo discovered cis-regulatory motifs. more...

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

202 Samples

Download data: CSV