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) 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

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(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) 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

(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

(Submitter supplied) Small RNAs have been studied in detail in Bacteria and Eukarya domain, but in the case of Archaea domain the knowledge is scarce and the physiological function of the majority is still uncertain. To extend the knowledge of sRNAs in Archaea domain and its possible role in the regulation of the nitrogen assimilation metabolism in haloarchaea, Haloferax mediterranei has been used as a model microorganism. more...

Organism:

Haloferax mediterranei

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20667

15 Samples

Download data: GFF3, TXT

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei in three culture media with different nitrogen sources: a) cells were grown stationary and exponentially on ammonium, b) cells were grown exponentially on nitrate, and c) cells were shifted to nitrogen starvation conditions. The main differences in the transcriptional profiles have been identified between the cultures with ammonium as nitrogen source and the cultures with nitrate or nitrogen starvation, supporting previous results which indicate the absence of ammonium as the factor causing the expression of genes involved in nitrate assimilation pathway.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL18892

8 Samples

Download data: TXT

(Submitter supplied) A potential origin that appears to stay dormant in its native host Haloferax volcanii lacking the main active origins becomes activated and competent for replication of the entire chromosome when integrated into the chromosome of the origin-deleted H. mediterranei.

Organism:

Haloferax mediterranei

Type:

Other

Platform:

GPL20667

1 Sample

Download data: TXT

(Submitter supplied) We have comprehensively explored the origin utilisation in Haloferax mediterranei. Here we report three active chromosomal origins by genome-wide replication profiling, and demonstrate that when these three origins are deleted, a dormant origin becomes activated.

Organism:

Haloferax mediterranei

Type:

Genome variation profiling by genome tiling array

Platform:

GPL20669

10 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei DF50 and ΔdeoR2 with induction by fructose comparing with the strains without this induction. Goal was to explore the effect of induction by fructose on Haloferax mediterranei.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL16102

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaEC strain, in which PHA synthase genes are knockouted. ΔphaEC strain is deficient in PHBV accumulation. Goal was to explore the PHBV biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL15465

6 Samples

Download data: LSR

(Submitter supplied) Transcriptional profiling of Haloferax mediterranei comparing control wild-type strain with ΔphaA1 strain, in which phaA1 gene are knockouted. ΔphaA1 strain can accumulate PHB only. Goal was to explore the PHA biosynthetic pathway and to determine their impact on primary metabolism in H. mediterranei.

Organism:

Haloferax mediterranei

Type:

Expression profiling by array

Platform:

GPL15465

4 Samples

Download data: LSR

(Submitter supplied) Arrays of this design have barcodes that begin with 16029586 or 2529586. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Haloferax mediterranei

3 Series

24 Samples

Download data: TXT

(Submitter supplied) the array was designed according to the former version genome of Haloferax mediterranei (CP001868.1-CP001871.1) Protocol: see manufacturer's web site www.nimblegen.com

Organism:

Haloferax mediterranei

1 Series

10 Samples

Download data: NDF, POS

(Submitter supplied) Arrays of this design have barcodes that begin with 16035154 or 2535154. The ID column represents the Agilent Probe name. *** The ID column includes the Agilent Probe Names. A different version of this platform with the Agilent Feature Extraction feature numbers in the ID column is assigned accession number GPL15465 Protocol: see manufacturer's web site at http://www.agilent.com/

Organism:

Haloferax mediterranei

1 Series

6 Samples

Download data: TXT

(Submitter supplied) Arrays of this design have barcodes that begin with 16035154 or 2535154. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Haloferax mediterranei

2 Series

10 Samples

Download data