txid2242[Organism:noexp] - GEO DataSets

Select item 2002007761.

Testing different rRNA removal methods in 4 species of model halophilic archaea

(Submitter supplied) We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.

Organism:: Haloferax volcanii; Haloferax mediterranei; Haloarcula hispanica; Halobacterium salinarum

Type:: Expression profiling by high throughput sequencing

4 related Platforms
39 Samples

Download data: TXT

Series

Accession:: GSE200776

ID:: 200200776

PubMed Full text in PMC Similar studies

Select item 2001825142.

Binding and Transcriptional profile of Halobacterium salinarum histone

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

Organism:: Halobacterium salinarum

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

Platforms:: GPL30532 GPL28343
64 Samples

Download data: TXT, WIG

Series

Accession:: GSE182514

ID:: 200182514

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Select item 2001824933.

Transcriptional profile of Halobacterium salinarum histone [RNA-seq]

(Submitter supplied) Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. more...

Organism:: Halobacterium salinarum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL30532
24 Samples

Download data: CSV, TXT

Series

Accession:: GSE182493

ID:: 200182493

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Select item 2001824924.

Binding profile of Halobacterium salinarum histone [ChIP-Seq]

(Submitter supplied) Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. more...

Organism:: Halobacterium salinarum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL28343
40 Samples

Download data: WIG

Series

Accession:: GSE182492

ID:: 200182492

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Select item 2001480655.

CdrL ChIP-seq data for the paper "CdrS is required for cell division site placement but not elongation in hypersaline-adapted archaea"

(Submitter supplied) Precise control of the cell cycle is central to the physiology of all cells. In prior work we demonstrated that archaeal cells maintain a constant cell size; however, the regulatory mechanisms underlying the cell cycle remain unexplored in this domain of life. In this study we use genetics, functional genomics, and quantitative imaging to identify and characterize the CdrSL gene regulatory network in a model species of archaea. more...

Organism:: Halobacterium salinarum

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL28343
16 Samples

Download data: BED, WIG

Series

Accession:: GSE148065

ID:: 200148065

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001040126.

H. salinarum R1 wildtype vs cyc-

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

Organism:: Halobacterium salinarum NRC-1; Halobacterium salinarum

Type:: Expression profiling by array

Platform:: GPL15637
2 Samples

Download data: TXT

Series

Accession:: GSE104012

ID:: 200104012

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000979337.

Discovery of transcription factor and regulatory network function through systematic deletion and quantitative phenotyping analysis in archaea

(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

Series

Accession:: GSE97933

ID:: 200097933

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000175158.

Coordination of frontline defense mechanisms under severe oxidative stress.

(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

Series

Accession:: GSE17515

ID:: 200017515

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000152769.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-2"

(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

Series

Accession:: GSE15276

ID:: 200015276

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001527510.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C"

(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

Series

Accession:: GSE15275

ID:: 200015275

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001527411.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-1"

(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

Series

Accession:: GSE15274

ID:: 200015274

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001527312.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B"

(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

Series

Accession:: GSE15273

ID:: 200015273

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001528213.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon

(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

Series

Accession:: GSE15282

ID:: 200015282

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001527214.

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "A"

(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...