GEO DataSets

(Submitter supplied) In eukaryotes, histone paralogues form obligate heterodimers such as H3/H4 and H2A/H2B that assemble into octameric nucleosome particles. Archaeal histones are dimeric and assemble on DNA into ‘hypernucleosome’ particles of varying sizes with each dimer wrapping 30 bp of DNA. These are likely composed of canonical and variant histone paralogues, but the function of these variants is poorly understood. more...

Organism:

Methanocaldococcus jannaschii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32760

3 Samples

Download data: BEDGRAPH

(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) The purpose of this experiment was to compare the transcriptomes of M. jannaschii using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown under H2-replete, H2-limited and H2-syntrophy conditions. The RNA-seq reads were mapped to both M. jannaschii and T. paralvinellae genomes using BBSplit from BBMap package. BBSplit is an aligner tool that bins sequencing reads by mapping to them multiple references simultaneously and separates the reads that map to multiple references to a special "ambiguous" file for each of them. more...

Organism:

Methanocaldococcus jannaschii; Thermococcus paralvinellae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24873 GPL24874

13 Samples

Download data: TXT

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

Organism:

Methanocaldococcus jannaschii; Saccharomyces cerevisiae

Type:

Expression profiling by array

4 related Platforms

42 Samples

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(Submitter supplied) Yeast strains expressing either GST-tagged or untagged Ypt1 were grown in either normal media or in media treated with 10mM DTT, to induce UPR A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. GeneticModification: GST tagged/untagged YPT1 Media: DTT present/absent in media

Organism:

Saccharomyces cerevisiae; Methanocaldococcus jannaschii

Type:

Expression profiling by array

Platform:

GPL14894

16 Samples

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(Submitter supplied) Strains lacking indicated genes were transformed with GST-YPT1. Ypt1p was IPd with anti-GST ab and associated rna was analyzed. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. GeneticModification: gene deleted from parent strain

Organism:

Saccharomyces cerevisiae; Methanocaldococcus jannaschii

Type:

Expression profiling by array

Platform:

GPL14894

8 Samples

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(Submitter supplied) Growth and transcriptional profiles of the barophilic methanarchaeon Methanocaldococcus jannaschii were studied at temperatures up to 98C and pressures up to 500 atm. Application of 500 atm of hyperbaric pressure shifted the optimal growth temperature upwards, and heat shock from 88C to 98C at 500 atm resulted in termination of growth. Pressure shock of M. jannaschii from 7.8 to 500 atm over 15-min, the first pressure upshift reported for a barophile, did not accelerate growth. more...

Organism:

Methanocaldococcus jannaschii

Type:

Expression profiling by array

Platform:

GPL3565

30 Samples

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(Submitter supplied) Barophilic growth of the hyperthermophilic methanarchaeon Methanocaldococcus jannaschii occurred when gas-substrate availability did not limit growth. In contrast, when growth was limited by gas transfer, no enhancement of growth was evident and a stress response was exhibited at both high and low pressure. A pressure-induced transcriptional response was evident, regardless of whether growth was enhanced by pressure. more...

Organism:

Methanocaldococcus jannaschii

Type:

Expression profiling by array

Platform:

GPL3565

13 Samples

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(Submitter supplied) Material is transferred from microtiter plate wells to the slide surface by an automated print head

Organism:

Methanocaldococcus jannaschii; Saccharomyces cerevisiae

3 Series

22 Samples

Download data: ADF

(Submitter supplied) Each sub-array contains blocks arranged 4 by 4 with each block running 22 rows by 20 columns. Protocol: Primers (Invitrogen) were designed for all 1738 open reading frames (ORFs) using Primer 3 software. Polymerase chain reaction was performed with 50 ng of genomic DNA, 0.8 uM of each forward and reverse primer, and 10 U of Taq DNA polymerase (New England Biolabs). Products were precipitated on 96 well plates with isopropanol and 3M sodium acetate at 4C and analyzed on a 0.8% agarose gel. more...

Organism:

Methanocaldococcus jannaschii

2 Series

39 Samples

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