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Items: 1 to 20 of 394

1.

Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Haloferax volcanii DS2
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL33952 GPL30888
63 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE248566
ID:
200248566
2.

Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii [CHIP-seq]

(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
3.

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

(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:
Expression profiling by high throughput sequencing
Platforms:
GPL33952 GPL30888
39 Samples
Download data: CSV
Series
Accession:
GSE248564
ID:
200248564
4.

The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Haloferax volcanii
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL31949
21 Samples
Download data: TXT, WIG
Series
Accession:
GSE240622
ID:
200240622
5.

The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

(Submitter supplied) Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that works as the major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL31949
9 Samples
Download data: TXT
Series
Accession:
GSE240621
ID:
200240621
6.

The TroR transcription factor genome-wide binding analysis in the halophilic archaeon Haloferax volcanii [ChIP-Seq]

(Submitter supplied) Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that directly binds the promoter of a set of genes involved in iron homeostasis meanwhile SirR is not a major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.
Organism:
Haloferax volcanii
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL31949
12 Samples
Download data: WIG
Series
Accession:
GSE240518
ID:
200240518
7.

Characterization of the zinc finger µ-protein HVO_0758 from Haloferax volcanii: biological roles, zinc binding, and NMR solution structure

(Submitter supplied) Transcriptome analysis based on total RNA-seq was performed on different Haloferax volcanii strains including mutants strains iincluding deletion strains for two small proteins. Differential expression analysis showed that a subset of genes were found to be regulated in the absence of the small proteins.
Organism:
Haloferax volcanii DS2
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33304
8 Samples
Download data: BW
Series
Accession:
GSE228855
ID:
200228855
8.

Revealing the small proteome of Haloferax volcanii by ribosome profiling and small-protein optimised mass spectrometry

(Submitter supplied) We present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii.
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL23691
6 Samples
Download data: BW, XLSX
Series
Accession:
GSE208086
ID:
200208086
9.

The chromatin landscape of the euryarchaeon Haloferax volcanii

(Submitter supplied) Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. more...
Organism:
Haloferax volcanii DS2
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platforms:
GPL32418 GPL30888
34 Samples
Download data: BIGWIG
Series
Accession:
GSE207470
ID:
200207470
10.

Genome-wide gene expression Haloferax volcanii under oxidative stress

(Submitter supplied) The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of H. volcanii upon treatment of NaOCl.
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32293
30 Samples
Download data: XLSX
Series
Accession:
GSE204840
ID:
200204840
11.

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
12.

TrmB-like family transcription factor OxsR regulates the oxidative stress response in Haloferax volcanii

(Submitter supplied) Haloarchaea tolerate high levels of reactive species that are naturally present in hypersaline environments. Hundreds of sRNAs, transcripts, and proteins are found altered in abundance when haloarchaea are exposed to reactive species, yet the regulators that control these responses are not well characterized. Here we report the function of Haloferax volcanii OxsR (redox stress responsive regulator, HVO_2970), a standalone  winged-helix DNA binding domain protein of the TrmB-like family. more...
Organism:
Haloferax volcanii
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL31949
24 Samples
Download data: BED
Series
Accession:
GSE196894
ID:
200196894
13.

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
14.

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
15.

Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

(Submitter supplied) Members of the third domain of life, the Archaea, are ubiquitous in all environments on Earth but remain understudied in many aspects including regulatory processes of the central dogma. Archaea present unique biology because they utilize a mosaic of molecular features from both Bacteria and Eukarya, along with unique features. The advent of a high-throughput view of the translation landscape via ribosome profiling in the Bacteria and the Eukarya has illuminated the complexity and previously underappreciated regulation of translation (i.e. more...
Organism:
Haloferax volcanii DS2
Type:
Other
Platform:
GPL27628
8 Samples
Download data: GFF, WIG
Series
Accession:
GSE138990
ID:
200138990
16.

Transcription analysis for the growth of Haloferax volcanii on L-alanine and ammonium chloride

(Submitter supplied) Identification of global gene expression profiling when Haloferax volcanii H26 strain is grown in minimal medium supplemented with two nitrogen sources, 10 mM L-alanine and 10 mM ammonium chloride.
Organism:
Haloferax volcanii
Type:
Expression profiling by array
Platform:
GPL21414
6 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE130934
ID:
200130934
17.

Characterization of the transcriptome of Haloferax volcanii with mixed RNA-Seq

(Submitter supplied) Recently a dRNA-Seq study with Haloferax volcanii has been published that led to the discovery of nearly 2800 novel transcription start sites for non-coding RNAs. However, the dRNA-Seq results are confined to the 5'-end of transcripts and does not contain any length information. Therefore, a major aim of the present RNA-Seq study was the elucidation of the lengths of the novel non-coding RNAs. A second aim was to analyze the operon structure of protein-coding genes. more...
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23691
1 Sample
Download data: WIG
Series
Accession:
GSE119686
ID:
200119686
18.

Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination

(Submitter supplied) Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. more...
Organism:
Haloferax volcanii
Type:
Other
Platform:
GPL23691
4 Samples
Download data: BED
Series
Accession:
GSE108201
ID:
200108201
19.

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
20.

Structural and functional adaptation of Haloferax volcanii TFEα/β

(Submitter supplied) Purpose: The Haloferax volcanii ∆tfeB strain provided a unique opportunity to study a putative role of TFEβ in the regulation of gene expression. Results: The deletion of the tfeB gene in H. volcanii results in the aberrant expression of approximately one third of all genes, consistent with its function as a basal transcription initiation factor. Interestingly, tfeB deletion particularly affects foreign genes including a prophage region. more...
Organism:
Haloferax volcanii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23691
4 Samples
Download data: XLSX
Series
Accession:
GSE101134
ID:
200101134
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