GEO DataSets

(Submitter supplied) Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”

Organism:

Pyrococcus furiosus

Type:

Other

Platform:

GPL28793

2 Samples

Download data: TXT, XLSX

(Submitter supplied) N4-acetylcytidine (ac4C) is an ancient and highly conserved RNA modification, present on tRNA, rRNA and recently investigated in eukaryotic mRNA. We report ac4C-seq, a chemical genomic method for single-nucleotide resolution, transcriptome-wide quantitative mapping of ac4C. While we did not find detectable ac4C sites in human and yeast mRNAs, ac4C was induced via ectopic overexpression of eukaryotic acetyltransferase complexes, invariably at a conserved sequence motif. more...

Organism:

Pyrococcus furiosus; Saccharomyces cerevisiae; Homo sapiens; Thermococcus sp. AM4; Thermococcus kodakarensis; Methanocaldococcus jannaschii; Saccharolobus solfataricus

Type:

Other

8 related Platforms

96 Samples

Download data: XLSX

(Submitter supplied) Pyrococcus yayanosii CH1 is the first and only obligate piezophilic hyperthermophilic microorganism discovered so far, that extends the physical and chemical limits of life on Earth and strengthens the idea of the existence of a hyperthermophilic biosphere in the depth of our planet. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses where performed in order to study the mechanisms implemented by the cell to face high hydrostatic pressure variations. more...

Organism:

Pyrococcus; Pyrococcus yayanosii; Pyrococcus furiosus

Type:

Expression profiling by array

Platform:

GPL20888

15 Samples

Download data: TXT

(Submitter supplied) CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, III) each recognize and target destruction of foreign invader nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. more...

Organism:

Pyrococcus furiosus

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL14794

4 Samples

Download data: BEDGRAPH

(Submitter supplied) A hybrid array setup containing WT Pyrococcus furiosus genes plus heterologous genes for engineered pathway producing 3HP from maltose and CO2 was used to study the impact of heterlogous pathway on native metabolic systems Four different experiments were run: 1) Pfu WT vs Pfu COM1; 2) Pfu COM1 vs MW56 (strain containing 3 heterologous genes from Metallosphaera sedula for production of 3HP); 3) Pfu COM1 vs MW76 at 72C before and after 3HP production; 4) MW76 at 72C before and after 3HP production at high agitation

Organism:

Pyrococcus furiosus COM1; Pyrococcus furiosus; Pyrococcus furiosus DSM 3638

Type:

Expression profiling by array

Platform:

GPL19860

14 Samples

Download data: GPR, TXT, XLSX

(Submitter supplied) Analysis of CRISPR RNAs from both total Pyrococcus furiosus RNA and those that co-purify with the Cmr complex, which has been predicted to be involved in RNA-mediated targeting of foreign RNAs in prokaryotes. Small RNAs (20 - 70 nts) were isolated either from total Pyrococcus furiosus RNA or RNAs isolated from immunopurified Cmr complexes. The RNAs were cloned and sequenced using the Illumina platform. more...

Organism:

Pyrococcus furiosus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14794

2 Samples

Download data: BEDGRAPH, SAM

(Submitter supplied) Small RNA Sequencing from Pyrococcus furiosus Keywords: Small RNA Analysis

Organism:

Pyrococcus furiosus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9384

1 Sample

Download data: TXT

(Submitter supplied) Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A-Dependent NAD(P)H Sulfur Oxidoreductase The hyperthermophilic archaeon Pyrococcus furiosus, uses carbohydrates as a carbon source and produces acetate, CO2 and H2 as end products. When S° is added to a growing culture, within 10 min the rate of H2 production rapidly decreases and H2S is detected. more...

Organism:

Pyrococcus furiosus; Pyrococcus furiosus DSM 3638

Type:

Expression profiling by array

Platform:

GPL4688

18 Samples

Download data: TXT

(Submitter supplied) The remarkable survival of the hyperthermophilic archaeon Pyrococcus furiosus to ionizing radiation was previously demonstrated. Using a time course study and whole-genome microarray analyses of mRNA transcript levels, the genes and regulatory pathways involved in the repair of lesions produced by ionizing irradiation (oxidative damage and DNA strand breaks) in P. furiosus were investigated. Data analyses showed that radA, encoding the archaeal homolog of the RecA/Rad51 recombinase, was moderately up regulated by irradiation and that a putative DNA-repair gene cluster was specifically induced by exposure to ionizing radiation. more...

Organism:

Pyrococcus furiosus

Type:

Expression profiling by array

Dataset:

GDS2469

Platform:

GPL3926

21 Samples

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Analysis of Pyrococcus furiosus cells exposed to 2.5 kGy of gamma radiation and then incubated at 90º C for up to 4 hours. At this dose, P. furiosus exhibits 75% survival. Results provide insight into the pathways involved in the repair of lesions produced by ionizing irradiation in P. furiosus.

Organism:

Pyrococcus furiosus

Type:

Expression profiling by array, log10 ratio, 2 agent, 6 time sets

Platform:

GPL3926

Series:

GSE5919

21 Samples

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(Submitter supplied) The P. furiosus full-genome microarray represented 2065 protein encoding genes. DNA fragments for spotting were produced by PCR. The array was constructed by designing oligonucleotide primers to span the most unique portions of each gene, averaging 350 nucleotides in length. A custom Perl program was written to select primers with the most desirable thermodynamic conditions possible for each gene using the Whitehead Institute's Primer3 program (version 3.09) as its core analysis engine. more...

Organism:

Pyrococcus furiosus

1 DataSet

1 Series

21 Samples

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(Submitter supplied) P. furiosus full-genome microarray numbered 2065 protein encoding genes, and 108 RNA genes (transfer RNAs, ribosomal RNAs, small RNAs). In addition, all "intergenic" regions of 60 nucleotides or larger were represented on the array (602 total). DNA fragments for spotting were produced by PCR. The array was constructed by designing oligonucleotide primers to span the most unique portions of each gene, averaging 350 nucleotides in length. more...

Organism:

Pyrococcus furiosus

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