GEO DataSets

(Submitter supplied) We demonstrate that the Cdc7/Dbf4-dependent histone modification, H3 threonine 45 phosphorylation (H3T45p), is specifically enriched at origins of replication, and highly transcribed genes involved in protein synthesis and glycolysis. Furthermore, we show that H3T45p also mediates polymerase recruitment and expression of these genes.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

4 Samples

Download data: BED

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL9377

30 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Nucleosomes are the primary unit of chromatin structure and inhibit key intracellular interactions which regulate how eukaryotic genetic information is read, including transcription factor (TF) binding to DNA. In theory, the sterics of nucleosome-DNA interactions could inhibit TF binding to all nucleosome-bound DNA. In reality, however, nucleosome inhibition of TF binding is variable both across a genome and even within a single nucleosome. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

6 Samples

Download data: XLS

(Submitter supplied) Nucleosomes are the primary unit of chromatin structure and inhibit key intracellular interactions which regulate how eukaryotic genetic information is read, including transcription factor (TF) binding to DNA. In theory, the sterics of nucleosome-DNA interactions could inhibit TF binding to all nucleosome-bound DNA. In reality, however, nucleosome inhibition of TF binding is variable both across a genome and even within a single nucleosome. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9377

12 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Nucleosomes are the primary unit of chromatin structure and inhibit key intracellular interactions which regulate how eukaryotic genetic information is read, including transcription factor (TF) binding to DNA. In theory, the sterics of nucleosome-DNA interactions could inhibit TF binding to all nucleosome-bound DNA. In reality, however, nucleosome inhibition of TF binding is variable both across a genome and even within a single nucleosome. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

12 Samples

Download data

(Submitter supplied) Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9377

16 Samples

Download data: XLSX

(Submitter supplied) Saccharomyces cerevisiae cannot metabolize non-glucose sugars including cellobiose, xylose, xylodextrins in nature, which are prevalent in plant cell wall. Here, one engineered S. cerevisiae strain, which expresses a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa; XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9377

26 Samples

Download data: XLSX

(Submitter supplied) Spt16-TAP ChIP-seq

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9377

12 Samples

Download data: WIG, XLSX

(Submitter supplied) It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive.  Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes.  Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. more...

Organism:

Saccharomyces mikatae; Saccharomyces cerevisiae; Saccharomyces paradoxus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21862 GPL9377 GPL21861

10 Samples

Download data: TXT

(Submitter supplied) Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. more...

Organism:

Synthetic plasmid; Saccharomyces cerevisiae; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

31 Samples

Download data: BW, FA, TXT

(Submitter supplied) Genome wide characterization of Mcm2-7 localization and origin activity for mrc1 and mcm mutant alleles.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

16 Samples

Download data: BED, WIG

(Submitter supplied) Saccharomyces cerevisiae cannot metabolize cellobiose in nature. Here, S. cerevisiae was engineered to achieve cellobiose utilization by introducing both a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (gh1-1) from Neurospora crassa. We sequenced mRNA from anaerobic exponential cultures of engineered S. cerevisiae grown on cellobiose or glucose as a single carbon source in biological triplicate. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9377

6 Samples

Download data: XLSX

(Submitter supplied) In this study we investigate the molecular physiology of the main S. cerevisiae commercial strain (PE-2) used on Brazilian bioethanol process under two distinct conditions: typical (TF) and flocculated (co-aggregated - FL) fermentation. Transcriptional machinery of PE-2 was assessed by high throughput sequencing-based methods (RNA-seq) during industrial fed-batch fermentations. Data from comparative analysis revealed distinct transcriptional profiles among conditions, characterized mainly by a deep gene repression on FL process.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9377

13 Samples

Download data: TXT

(Submitter supplied) Ribosome profiling data reports on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9377

10 Samples

Download data: TXT

(Submitter supplied) In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we identify two prevalent RPG promoter types, both characterized by upstream binding of the general transcription factor (TF) Rap1 followed by the RPG-specific Fhl1/Ifh1 pair, with one type also binding the HMG-B protein Hmo1. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL9377

11 Samples

Download data: BW

(Submitter supplied) Using a technique based on the ability of CMC to specifically label pseudouridines and to stop reverse transcriptase, we provide a transcriptome-wide map of pseudouridylation in S. cerevisiae under log phase and heat shock conditions

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL9377

16 Samples

Download data: TXT

(Submitter supplied) Asf1, through its histone chaperone activity, helps chromatin closing/opening during DNA replication, repair, recombination and transcription. Despite extensive research on Asf1-mediated physiological functions, a genome-wide localization map is lacking, limiting our knowledge of chromosomal features targeted by Asf1. We present a high-resolution genome-wide map of Asf1, localizing at essentially all pol III-transcribed genes, highly active pol II-transcribed genes and heterochromatic features. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

3 Samples

Download data: BEDGRAPH

(Submitter supplied) A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL9377

22 Samples

Download data: TXT

(Submitter supplied) Paired-end sequencing study of nucleosomes from MNase-digested nuclei.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9377 GPL13821

8 Samples

Download data: BW