Similar studies for GEO DataSets (Select 200204840) - GEO DataSets

(Submitter supplied) The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. more...

Organism:: Haloferax volcanii DS2

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

Platform:: GPL33952
24 Samples

Download data: BEDGRAPH, TXT

Series

Accession:: GSE248565

ID:: 200248565

PubMed Similar studies

Select item 2002485644.

Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

Organism:: Haloferax volcanii DS2

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL33952 GPL30888
39 Samples

Download data: CSV

Series

Accession:: GSE248564

ID:: 200248564

PubMed Similar studies

Select item 2001864155.

Genome-wide binding (ChIP-Seq) of histone-like protein (HstA) of Haloferax volcanii

(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

Series

Accession:: GSE186415

ID:: 200186415

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000472016.

H. salinarum TrmB dynamics

(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

Series

Accession:: GSE47201

ID:: 200047201

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000775897.

GlpR functions as a global DeoR-type regulator of metabolic gene transcription in the haloarchaeon Haloferax volcanii

(Submitter supplied) Investigation of gene expression in ∆glpR mutant strains vs wild type in response to glycerol and glucose.

Organism:: Haloferax volcanii

Type:: Expression profiling by array

Platform:: GPL21414
12 Samples

Download data: PAIR

Series

Accession:: GSE77589

ID:: 200077589

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000276378.

S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics

(Submitter supplied) Protein S-thiolation is a post-translational thiol-modification that controls redox-sensing transcription factors and protects active site cysteine residues against irreversible oxidation. In Bacillus subtilis the MarR-type repressor OhrR was shown to sense organic hydroperoxides via formation of mixed disulfides with the redox buffer bacillithiol (Cys-GlcN-Malate, BSH), termed as S-bacillithiolation. more...

Organism:: Bacillus subtilis subsp. subtilis str. 168

Type:: Expression profiling by array

Platform:: GPL10901
3 Samples

Download data: TXT

Series

Accession:: GSE27637

ID:: 200027637

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000297069.

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon

(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

Series

Accession:: GSE29706

ID:: 200029706

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002970510.

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon [ChIP-chip data]

(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

Series

Accession:: GSE29705

ID:: 200029705

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002970411.

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon [gene expression data]

Organism:: Halobacterium salinarum NRC-1

Type:: Expression profiling by array

Platform:: GPL13682
48 Samples

Download data: CSV, TXT

Series

Accession:: GSE29704

ID:: 200029704

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001353112.

Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium

(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

Series

Accession:: GSE13531

ID:: 200013531

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001352913.

Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose

Organism:: Halobacterium salinarum NRC-1

Type:: Expression profiling by array

Platform:: GPL3739
46 Samples

Download data: CSV

Series

Accession:: GSE13529

ID:: 200013529

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001349814.

Halobacterium salinarum NRC-1 VNG1451C transcription factor ChIP-chip with and without carbon sources

Organism:: Halobacterium salinarum NRC-1

Type:: Genome binding/occupancy profiling by array

Platform:: GPL4664
28 Samples

Download data: CSV

Series

Accession:: GSE13498

ID:: 200013498

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20010389315.

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

(Submitter supplied) We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. more...

Organism:: Haloferax volcanii DS2

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL21976
16 Samples

Download data: TXT

Series

Accession:: GSE103893

ID:: 200103893

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20005901016.

Genome-wide binding site profiling of NdgR in Streptomyces coelicolor

(Submitter supplied) We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).

Organism:: Streptomyces coelicolor

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

Platform:: GPL18886
1 Sample

Download data: GFF

Series

Accession:: GSE59010

ID:: 200059010

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003398017.

RosR is a haloarchaeal-specific transcription factor required for the response to extreme oxidative stress in Halobacterium salinarum NRC-1.

(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

Series

Accession:: GSE33980

ID:: 200033980

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20015889118.

Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

(Submitter supplied) Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. more...

Organism:: Haloferax volcanii DS2

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21976
16 Samples

Download data: TXT, XLSX

Series

Accession:: GSE158891

ID:: 200158891

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20014806519.

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...