GEO DataSets

(Submitter supplied) Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse subset of natural isolates of the Saccharomyces cerevisiae yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26171

32 Samples

Download data: TXT

(Submitter supplied) Comparison of translation efficiency in S. cerevisiae, S. paradoxus, and their F1 hybrid.

Organism:

Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces cerevisiae x Saccharomyces paradoxus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17601 GPL17602 GPL13821

12 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution, synthetic biology, gene expression regulation, intracellular biophysics, and more. However, this phenomenon hasn't been quantified yet at a genomic level. Nevertheless, methodologies for studying translation (e.g. ribosome footprints) are usually calibrated to capture only single ribosome protected footprints (mRPFs) and thus limited in their ability to detect ribosome queuing. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

3 Samples

Download data: TSV

(Submitter supplied) Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

8 Samples

Download data: TXT

(Submitter supplied) We characterize the translational and transcriptional programs induced by MetR and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S. cerevisiae as the model organism. Using ribosomal profiling and RNA-seq, we systematically compared the translational and transcriptional profiles of cells growing in the normal and methionine restricted media. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: WIG

(Submitter supplied) Saccharomyces cerevisiae CEN.PK113-1A was grown in glucose-limited chemostat culture with 0%, 0.5%, 1.0%, 2.8% or 20.9% O2 in the inlet gas (D= 0.10 /h, pH5, 30C).

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

22 Samples

Download data: CEL

(Submitter supplied) In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13254

196 Samples

Download data: FTR, PAIR

(Submitter supplied) The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

36 Samples

Download data: CEL

(Submitter supplied) Extensive transcriptional heterogeneity revealed by isoform profiling

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

18 Samples

Download data: TXT

(Submitter supplied) Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

3 Samples

Download data: TXT

(Submitter supplied) Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units positioned across multiple loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. It remains elusive whether expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may have functional roles in translation control. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

7 Samples

Download data: TXT

(Submitter supplied) Production of D-xylonate in the yeast S. cerevisiae represents an example of bioprocess development for more sustainable production of value-added chemicals from cheap raw material or waste. Previously it was shown that the production of D-xylonate led to its significant intracellular accumulation and to dramatic loss of viability during the production process. In order to identify the physiological or pathological responses associated with D-xylonate production, we performed a time-course transcriptome analysis of D-xylonate production in yeast cultivated in a bioreactor. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL17988

36 Samples

Download data: XYS

(Submitter supplied) Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

176 Samples

Download data: FA, GTF, TXT

(Submitter supplied) Experiments for optimization of the ribosome profiling protocol using C. elegans lysates. We report that optimizing the cutting accuracy to a narrow window of 28-30 nucleotides when PAGE-purifying the ribosome-protected fragments (RPFs) significantly improves the quality of the RPF library. In addition, we find that purifying monosomes by sucrose gradient fractionation clearly removed more contaminating ribosomal RNA from the samples compared to the purification by gel filtration columns.

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL13657

8 Samples

Download data: TSV

(Submitter supplied) Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

96 Samples

Download data: TXT

(Submitter supplied) Ribosome profiling provides an opportunity to not only assess how the relative abundance of ribosome association with mRNAs changes in different conditions, but to look more closely at where along mRNAs those ribosomes bind. Here, we used ribosome profiling to calculate the ribosome polarity scores and changes in ribosome footprint read density in both aggregate and gene-specific ways. We profiled a time course of acute glucose starvation followed by glucose readdition and a multi-day growth course through the diauxic shift into stationary phase. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

21 Samples

Download data: XLSX

(Submitter supplied) Saccharomyces cerevisiae is unique among yeasts for its ability to grow rapidly in the complete absence of oxygen. S. cerevisiae is therefore an ideal eukaryotic model to study physiological adaptation to anaerobiosis. Recent transcriptome analyses have identified hundreds of genes that are transcriptionally regulated by oxygen availability but the relevance of this cellular response has not been systematically investigated at the key control level of the proteome. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL4992

1 Sample

Download data: XLS

(Submitter supplied) We present ribosome profiling and RNA-Seq data for the wild type BY4742 S. cerevisiae strain, and strains with the complete individual deletions of the TMA46, STM1 and YGR054W genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

32 Samples

Download data: CSV, TSV

(Submitter supplied) We present ribosome profiling and RNA-Seq data for the wild type BY4742 S. cerevisiae strain, and strains with the complete individual deletions of the GIR2 and PUB1 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

26 Samples

Download data: CSV, TSV

(Submitter supplied) Six strains of Saccharomyces cerevisiae were grown in four different environments representing a continuum of rich and poor natural conditions Keywords: Stress response, genetic diversity

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2682

91 Samples

Download data