GEO DataSets

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

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL27060 GPL28445

9 Samples

Download data: WIG

(Submitter supplied) In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27060

3 Samples

Download data: CSV

(Submitter supplied) In this study, an exoribonuclease was analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes. Mapping of most reads to mRNAs underlines the role of exosome in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5’-ends of genes suggests simultaneous binding of both RNA ends by the S. more...

Organism:

Saccharolobus solfataricus

Type:

Other

Platform:

GPL28445

6 Samples

Download data: WIG

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterized how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27828

3 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27815 GPL27828

12 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

4 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27828

2 Samples

Download data: BW, CSV

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

4 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27828

4 Samples

Download data: BW

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

Organism:

Saccharolobus solfataricus P2; Saccharolobus solfataricus

Type:

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

Platforms:

GPL28984 GPL27828 GPL27815

84 Samples

Download data: BAM, BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

9 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

6 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

6 Samples

Download data: BW

(Submitter supplied) Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27828 GPL27815

16 Samples

Download data: BW

(Submitter supplied) Genome-wide occupancy of the basal transcription machinery in Saccharolobus solfataricus strain P2 (Sulfolobus solfataricus) after hydrogen peroxide treatment Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27815

16 Samples

Download data: BW

(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:

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

Type:

Other

8 related Platforms

96 Samples

Download data: XLSX

(Submitter supplied) Purpose: To identify the genome binding sites of Cren7 and Sso7D, and to determine whether binding patterns differ between wild type and an epigenetically evolved strain in which they are heritably hypomethylated. Because methylated residues were solvent facing, it was predicted that binding patterns would not change between the strains. Methods: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina Hiseq. more...

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27594

24 Samples

Download data: BEDGRAPH

(Submitter supplied) Hydroxyurea (HU) is toxic to Sulfolobus cells. To address the basis of the HU toxicity, we performed transcriptome analyses on untreated cells and cells following exposure to 5 mM HU for 4 hours.

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19085

2 Samples

Download data: TXT

(Submitter supplied) Extremely thermoacidophilic Crenarchaeota belonging to the family Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. However, the pH extremes of these habitats often exceed the acid tolerance of type species and strains. Here, experimental evolution was used to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high temperature serial passage while culture acidity was gradually increased. more...

Organism:

Saccharolobus solfataricus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21286

6 Samples

Download data: XLSX

(Submitter supplied) We report the in vivo binding of transcription factor MerR in the presence and absence of mercury as measured by ChIPSeq.

Organism:

Saccharolobus solfataricus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19085

3 Samples

Download data: TRACK, TXT