GEO DataSets

(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) 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

(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

(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

(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

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

Organism:

Halobacterium salinarum; Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL15637

2 Samples

Download data: TXT

(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

(Submitter supplied) RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23553

6 Samples

Download data: TXT

(Submitter supplied) We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

12 Samples

Download data: TXT

(Submitter supplied) Previous work identified the winged helix-turn-helix DNA binding transcription factor (TF) RosR (encoded by VNG0258H gene), which dynamically regulates expression of more than 300 genes in response to oxidative stress in Halobacterium salinarum (Sharma 2012). RosR is required for survival of oxidants from multiple sources (e.g. H2O2 and paraquat), as deletion mutants are impaired for ROS outgrowth. Genes directly and indirectly controlled by RosR in response to ROS encode macromolecular repair functions. In the current study, we ask which of these genes are direct targets of RosR regulation. Dynamic chromatin immunoprecipitation combined with microarray (ChIP-chip) analysis validates that genes encoding these functions are direct targets of RosR binding and control. In addition, new RosR direct target genes are identified, including those encoding central cellular functions and a surprisingly high number of other TFs. The majority of the 252 sites throughout the genome are RosR-bound in the absence of stress and cleared of RosR binding in the presence of H2O2. However, binding is dynamic, with promoter-specific differences in the timing of RosR-DNA release and re-binding relative to ROS exposure.

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL18848

20 Samples

Download data: TXT

(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:

GPL17005 GPL13426

58 Samples

Download data: TXT

(Submitter supplied) Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1.

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13426

34 Samples

Download data: TXT

(Submitter supplied) We validated context dependent regulation by two FFRPs AsnC and VNG1237C by deleting the FFRP and testing the effect on downstream target genes. For validtion of AsnC condition specific regulation we grew wild-type and delta-AsnC in the presence of 4mM paraquat (PQ) and samples at 1 and 160 minutes post addition of this sub-lethal dose of PQ. For validation of VNG1237C we grew wild-type and delta-VNG1237C in a standard growth curve sampling at OD 0.18 and 1.15.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL17005

24 Samples

Download data: TXT

(Submitter supplied) To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

8 Samples

Download data: TXT

(Submitter supplied) Halobacterium salinarum is an extreme halophilic archaeon adapted to total salinities upwards of 4 M. Here we studied gene expression in H. salinarum grown in ten ion composition media that vary in two major aspects of ion composition: [NaCl] and Mg:K ratio.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

20 Samples

Download data: TXT

(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

(Submitter supplied) The microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others’ fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD) on a population’s growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13682

32 Samples

Download data: CSV, TXT

(Submitter supplied) As part of a comprehensive post-genomic investigation of the model archaeon Halobacterium sp. NRC-1, we used whole genome DNA microarrays to compare transcriptional profiles of cells grown anaerobically via arginine fermentation versus cells either respiring aerobically in the presence of oxygen or anaerobically using trimethylamine N-oxide (TMAO) as a terminal electron acceptor.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL15637

5 Samples

Download data: TXT

(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

(Submitter supplied) Halobacterium salinarum is a halophillic archea that is capable of sustaining growth despite dramatic changes to the concentration of ions in its extracellular environment. Here we studied H. salinarum's specific adaptation response to the transition metal copper.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13682

49 Samples

Download data: CSV