GEO DataSets

(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) RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. more...

Organism:

Thermococcus barophilus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33349

9 Samples

Download data: CSV, 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:

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

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) In ordet to understand in vivo role of uncharacterized DNA-binding protein (TON_1525) in T. onnurineus NA1, TON_1525 gene deletion mutant was constructed. Also transcriptome analysis was perfomed between wild type and mutant strains to measure changed expression profile of genes by deletion of TON_1525 gene under CO supplemented medium.

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: XLSX

(Submitter supplied) Previously, we reported that the TON_1525 (T55I) (designated as MC11) strain showed superior activity in CO oxidation than the wild-type strain. To understand the in vivo role of TON_1525 in this strain on CO-supplemented medium, transcriptome changes were investigated.

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

6 Samples

Download data: XLSX

(Submitter supplied) Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life. more...

Organism:

Methanosarcina acetivorans C2A

Type:

Other

Platform:

GPL33336

12 Samples

Download data: TXT

(Submitter supplied) Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) from TrmB in the halophilic archaeon Haloarcula hispanica in the presence and absense of glucose.

Organism:

Haloarcula hispanica ATCC 33960

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33237

16 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Transcripome profiling (RNA-seq) of TrmB in the halophilic archaeon Haloarcula hispanica in the presence and absense of glucose after 24 hours.

Organism:

Haloarcula hispanica ATCC 33960

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33236

32 Samples

Download data: CSV

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

Organism:

Haloarcula hispanica ATCC 33960

Type:

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

Platforms:

GPL33236 GPL33237

48 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Methanogens inhabit euxinic (sulfide-rich) or ferruginous (iron-rich) environments that promote the precipitation of transition metals as metal sulfides, such as pyrite, reducing metal or sulfur availability. Such environments have been common throughout Earth’s history raising the question as to how anaerobes obtain(ed) these elements for the synthesis of enzyme cofactors. Here, we show a methanogen can synthesize molybdenum nitrogenase metallocofactors from pyrite as the source of iron and sulfur, enabling nitrogen fixation. more...

Organism:

Methanococcus maripaludis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32793

12 Samples

Download data: TXT

(Submitter supplied) To determine the difference in gene expression of SNJ2 genes with and without MMC treatment, Natrinema sp. J7-1 was incubated to middle exponential phase (OD600=0.6-0.8) in Halo-2 medium and treated with MMC

Organism:

Natrinema sp. J7-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33092

11 Samples

Download data: TXT

(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