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Items: 1 to 20 of 511

1.

The Replication Kinase Cdc7 Marks Histones to Regulate Biosynthesis Genes

(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
Series
Accession:
GSE43737
ID:
200043737
2.

Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription

(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
Series
Accession:
GSE92468
ID:
200092468
3.

Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [ChIP-seq]

(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
Series
Accession:
GSE92467
ID:
200092467
4.

Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [RNA-seq]

(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
Series
Accession:
GSE90669
ID:
200090669
5.

Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [MNase-seq]

(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
Series
Accession:
GSE90458
ID:
200090458
6.

Impact of xylose feeding on transcriptome profiles of anaerobically fed-batch xylodextrins consumption in Saccharomyces cerevisiae

(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
Series
Accession:
GSE69448
ID:
200069448
7.

Impact of plant cell wall derived sugars on transcriptional and post-transcriptional control in Saccharomyces cerevisiae

(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
Series
Accession:
GSE69404
ID:
200069404
8.

Genome-wide profiling of histone chaperone FACT in Saccharomyces cerevisiae

(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
Series
Accession:
GSE83086
ID:
200083086
9.

Translation elongation mediated quality control of integral membrane protein synthesis

(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
Series
Accession:
GSE75004
ID:
200075004
10.

Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

(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 paradoxus; Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL9377 GPL21862 GPL21861
10 Samples
Download data: TXT
Series
Accession:
GSE81320
ID:
200081320
11.

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

(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:
Saccharomyces cerevisiae; Mus musculus; Synthetic plasmid
Type:
Genome binding/occupancy profiling by high throughput sequencing
4 related Platforms
31 Samples
Download data: BW, FA, TXT
Series
Accession:
GSE65889
ID:
200065889
12.

Mcm2-7 is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of its DNA Gate

(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
Series
Accession:
GSE38032
ID:
200038032
13.

Transcriptional reprogramming of engineered cellobiose-utilizing Saccharomyces cerevisiae in response to cellobiose revealed by RNA-Seq

(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
Series
Accession:
GSE54825
ID:
200054825
14.

Genome-wide transcriptional analysis of PE-2 strain of Saccharomyces cerevisiae

(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
Series
Accession:
GSE41834
ID:
200041834
15.

Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation

(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
Series
Accession:
GSE63789
ID:
200063789
16.

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

(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
Series
Accession:
GSE61596
ID:
200061596
17.

PSI-seq to Identify Sites of Pseudouridylation in S. cerevisiae

(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
Series
Accession:
GSE60445
ID:
200060445
18.

Genome-wide targets of conserved histone chaperone Asf1 in budding yeast

(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
Series
Accession:
GSE40717
ID:
200040717
19.

Ribosome profiling upon glucose starvation in S. cerevisiae

(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
Series
Accession:
GSE56622
ID:
200056622
20.

Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae

(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
Series
Accession:
GSE49512
ID:
200049512
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