GEO DataSets

(Submitter supplied) DNA deamination occurs constantly in a cell and causes DNA damage. As this damage can be deleterious, organisms have evolved many systems to eliminate it. Deamination of cytosine, guanine, adenine, and 5-methylcytosine results in the formation of uracil, xanthine, hypoxanthine, and thymine, respectively. Sodium bisulfite is a kind of DNA deaminating agent that can increase the frequency of DNA deamination in cells. more...

Organism:

Haloferax volcanii DS2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30888

12 Samples

Download data: TXT

(Submitter supplied) Nucleases, i.e. enzymes that catalyze the hydrolysis of phosphodiester bonds in nucleic acids, are essential tools in molecular biology and biotechnology. Staphylococcus aureus nuclease (MNase) is particularly interesting due to its thermostability and Ca2+-dependence, making it the prime choice for applications where nuclease modulation is critical, such as ribosome profiling in bacteria and halophilic archaea. more...

Organism:

Haloferax volcanii

Type:

Other

Platform:

GPL32165

6 Samples

Download data: CSV, TXT

(Submitter supplied) Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell such as the accurate control of the metal homeostasis. more...

Organism:

Haloferax mediterranei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20667

6 Samples

Download data: TXT

(Submitter supplied) PRO-seq experiments in multiple organisms. Also, PRO-seq experiment of Nelfb and Nelfe degron mESC in serum/LIF with or without dTAG-13. 

Organism:

Daphnia pulex; Strongylocentrotus purpuratus; Sphaeroforma arctica; Haloferax mediterranei; Dryas iulia; Nematostella vectensis; Escherichia coli; Mus musculus; Perkinsus marinus; Dictyostelium discoideum; Capsaspora owczarzaki; Creolimax fragrantissima

Type:

Other

12 related Platforms

46 Samples

Download data

(Submitter supplied) The transcriptional analysis of the HM26-ΔSm1 deletion mutant versus the parental strain HM26 was performed under nitrogen and carbon starvation for 120 h. These contrasts allow us to analyze the effect that the deletion of the Sm1 motif has under these conditions and, therefore, allow us to know which genes are regulated by the Lsm protein under the conditions analyzed.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL18892

8 Samples

Download data: TXT

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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

(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:

Halobacterium salinarum; Haloferax volcanii; Haloferax mediterranei; Haloarcula hispanica

Type:

Expression profiling by high throughput sequencing

4 related Platforms

39 Samples

Download data: TXT

(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

(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

(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

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei DglnA and HM26 strains in two different culture media: a) cells were grown exponentially on complex media + 40 mM Gln, b) cells were shifted to nitrogen starvation conditions (72h). In the Nsta(∆glnA)-Cx and Nsta-Cx contrasts, glnA2 was up-regulated, and glnA3 did not show any difference. Therefore, glnA2 and glnA3 were unable to compensate lack of glnA because either they do not properly encode GS or are not expressed under the same conditions.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL18892

8 Samples

Download data: TXT