GEO DataSets

(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

(Submitter supplied) We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth. While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression. This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

79 Samples

Download data: CSV

(Submitter supplied) We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth. While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression. This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

23 Samples

Download data: CSV

(Submitter supplied) We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth. While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression. This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

28 Samples

Download data: CSV

(Submitter supplied) We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth. While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression. This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

28 Samples

Download data: CSV

(Submitter supplied) Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

42 Samples

Download data: CSV

(Submitter supplied) Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

46 Samples

Download data: CSV

(Submitter supplied) Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum NRC-1

Type:

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

7 related Platforms

202 Samples

Download data: CSV, PAIR

(Submitter supplied) Halobacterium salinarum NRC-1 was grown in CM media, at 37oC in a waterbath with agitation of 125 rpm under constant light. Analysis of transcriptional changes during growth, in addition to mapping of transcriptome structure under the same conditions, provided interesting insights about regulatory logic within prokaryotic coding regions.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

52 Samples

Download data: CSV

(Submitter supplied) By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

50 Samples

Download data: CSV

(Submitter supplied) By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

52 Samples

Download data: CSV

(Submitter supplied) By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

38 Samples

Download data: CSV

(Submitter supplied) By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum NRC-1; Halobacterium salinarum

Type:

Expression profiling by array

Platform:

GPL3739

38 Samples

Download data: CSV

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

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

214 Samples

Download data: CSV

(Submitter supplied) By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum NRC-1; Halobacterium salinarum

Type:

Expression profiling by array

Platform:

GPL3739

36 Samples

Download data: CSV

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

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

200 Samples

Download data: CSV

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

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

170 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of gap was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0019h was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of sop2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV