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Items: 1 to 20 of 3817

1.

Rprd Proteins Control Transcription In Human Cells

(Submitter supplied) Regulation of transcription is an essential process that allows the cell to respond to various internal and external signals. RNA Polymerase II (Pol II) activity is controlled by a number of factors which bind to the C-terminal domain (CTD) of its largest subunit, RPB1, and stimulate or supress RNA synthesis. Here, we demonstrate that members of the RPRD family of CTD-interacting proteins, RPRD1A, RPRD1B and RPRD2, act as negative regulators of transcription. more...
Organism:
Saccharomyces cerevisiae; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20276
8 Samples
Download data: BIGWIG
Series
Accession:
GSE178213
ID:
200178213
2.

Spo11 generates gaps through concerted cuts at sites of topological stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae; [Candida] glabrata; Saccharomyces kudriavzevii
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL29937 GPL29940 GPL29941
71 Samples
Download data: TAR, TXT, WIG
Series
Accession:
GSE171046
ID:
200171046
3.

Spo11 generates gaps through concerted cuts at sites of topological stress [dDSB]

(Submitter supplied) Meiotic recombination is essential for proper meiotic chromosome segregation and fertility, and is initiated by programmed DNA double-strand breaks (DSBs) introduced by Spo11, a eukaryotic homolog of archaeal topoisomerase VIA. Here we report the discovery of hitherto uncharacterized Spo11-induced lesions, small gaps from 34 bp to several hundred bp, which are generated by coordinated pairs of DSBs (double DSBs or dDSBs). more...
Organism:
Saccharomyces cerevisiae; Saccharomyces kudriavzevii
Type:
Other
Platforms:
GPL29940 GPL29941
63 Samples
Download data: TAR, TXT, XLSX
Series
Accession:
GSE171042
ID:
200171042
4.

Spo11 generates gaps through concerted cuts at sites of topological stress [Top2]

(Submitter supplied) Meiotic recombination is essential for proper meiotic chromosome segregation and fertility, and is initiated by programmed DNA double-strand breaks (DSBs) introduced by Spo11, a eukaryotic homolog of archaeal topoisomerase VIA. Here we report the discovery of hitherto uncharacterized Spo11-induced lesions, small gaps from 34 bp to several hundred bp, which are generated by coordinated pairs of DSBs (double DSBs or dDSBs). more...
Organism:
Saccharomyces cerevisiae; [Candida] glabrata
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL29937
8 Samples
Download data: TXT, WIG, XLSX
Series
Accession:
GSE169760
ID:
200169760
5.

Checkpoint-mediated DNA polymerase e exonuclease activity curbing counteracts resection-driven fork collapse

(Submitter supplied) DNA polymerase epsilon (Pole) carries out leading strand synthesis with high fidelity owing to its exonuclease activity. Pole polymerase and exonuclease activities are in balance, due to partitioning of nascent strands between catalytic sites, so that net end resection occurs when synthesis is impaired. Stalling of chromosomal DNA synthesis activates replication checkpoint kinases, required to preserve the functional integrity of replication forks. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
46 Samples
Download data: BED, BW
Series
Accession:
GSE156480
ID:
200156480
6.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

(Submitter supplied) A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however, is the need of tailored protocols to map each modification type individually. Here, we present a new approach that uses direct RNA nanopore sequencing to identify diverse RNA modification types present in native RNA molecules. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL25739
24 Samples
Download data: CSV, TSV
Series
Accession:
GSE148603
ID:
200148603
7.

Development of High-throughput 5Pseq and detection of ribosome stalls at termination level in Saccharomyces cerevisiae

(Submitter supplied) We developed a high throughput 5’P sequencing approach (HT-5PSeq) to investigate 5'P mRNA degradome in relation with translation process. This approach is easy and scalable; and uses an affordable rRNA depletion based on duplex-specific nuclease treatment. We use it to investigate in vivo ribosome stalls in S. cerevisiae and S. pombe at single nucleotide resolution. We investigate the 5’P degradation profiles associated to ribosome pausing, its regulation in stress conditions and the relative poly(A) length of mRNA degradation intermediates.
Organism:
Saccharomyces cerevisiae; Schizosaccharomyces pombe
Type:
Other
Platforms:
GPL20584 GPL19756
20 Samples
Download data: BEDGRAPH
8.

UBB+1-induced activation of autophagy reduces cytotoxicity of amyloid-β in yeast

(Submitter supplied) UBB+1 is a mutated version of ubiquitin B caused by a transcriptional frameshift. The accumulation of UBB+1, has been linked to ubiquitin-proteasome system (UPS) dysfunction and neurodegeneration. Alzheimer’s disease (AD) is the most common form of neurodegeneration and accumulation of amyloid β (Aβ) in the brain is a prominent neuropathological feature of AD. In our previous study, we found that low expression of UBB+1 could protect cells against several stresses during chronological aging. more...
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL2529
8 Samples
Download data: CEL
Series
Accession:
GSE129688
ID:
200129688
9.

Selectivity of mRNA degradation by autophagy in yeast

(Submitter supplied) Synthesis and degradation of cellular constituents must be balanced to maintain cellular homeostasis, especially during adaptation to environmental stress. The role of autophagy in the degradation of proteins and organelles is well-characterized. However, autophagy-mediated RNA degradation in response to stress and the potential preference of specific RNAs to undergo autophagy-mediated degradation have not been examined. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL21656
22 Samples
Download data: TXT
Series
Accession:
GSE149016
ID:
200149016
10.

Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs

(Submitter supplied) Recent single-cell studies have revealed that yeast stress response involves multiple transcription factors that are temporally activated in pulses. However, it remains largely unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. more...
Organism:
[Candida] glabrata; Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL29410 GPL26171
36 Samples
Download data: CSV
Series
Accession:
GSE161373
ID:
200161373
11.

Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites

(Submitter supplied) Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL7250
22 Samples
Download data: BAR, CEL, TXT
Series
Accession:
GSE147452
ID:
200147452
12.

A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels

(Submitter supplied) The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
4 Samples
Download data: MTX, TSV
Series
Accession:
GSE165686
ID:
200165686
13.

Disturbed intramitochondrial phosphatidic acid transport impairs cellular stress signaling

(Submitter supplied) Lipid transfer proteins of the Ups1/PRELID1 family facilitate the transport of phospholipids across the intermembrane space of mitochondria in a lipid-specific manner. Heterodimeric complexes of yeast Ups1/Mdm35 or human PRELID1/TRIAP1 shuttle phosphatidic acid (PA) synthesized in the endoplasmic reticulum (ER) to the inner membrane, where it is converted to cardiolipin (CL), the signature phospholipid of mitochondria. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
12 Samples
Download data: TSV
Series
Accession:
GSE160861
ID:
200160861
14.

Global repression driven by RNA polymerase II stalling in yeast

(Submitter supplied) In multicellular eukaryotes, RNA polymerase (pol) II pauses transcription ~30-50 bp after initiation, and involves DSIF and other factors. While the budding yeast Saccharomyces has its transcription mechanisms mostly conserved with other eukaryotes, it appears to lack this fundamental promoter-proximal pausing. However, we now discover that acute stress (e.g., peroxide) causes most yeast genes, including constitutive and stress-induced genes, to manifest two distinct pausing or stall sites during the early elongation phase of Pol II transcription. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
104 Samples
Download data: BW, TSV
Series
Accession:
GSE151348
ID:
200151348
15.

Discovery of a new gene target enabling carotenoids improvement of recombinant Saccharomyces cerevisiae using ethanol-induced adaptive laboratory evolution

(Submitter supplied) Adaptive laboratory evolution (ALE) is an increasingly popular technique, which allows screening strains with excellent phenotype through accumulative positive changes. However, little strategy based on ALE has been previously reported about improving carotenoids yield in S. cerevisiae. Herein, a new ethanol-induced ALE was successfully applied to boost carotenoids accumulation in a carotenoid producer BL03-D-4. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
2 Samples
Download data: TXT, XLSX
Series
Accession:
GSE164470
ID:
200164470
16.

Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors

(Submitter supplied) Phosphatidylethanolamine made in mitochondria has long been recognized as an important precursor for phosphatidylcholine production that occurs in the endoplasmic reticulum (ER). Recently, the strict mitochondrial localization of the enzyme that makes PE in the mitochondrion, phosphatidylserine decarboxylase 1 (Psd1), was questioned. Since a dual localization of Psd1 to the ER would have far-reaching implications, we initiated our study to independently re-assess the subcellular distribution of Psd1. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
24 Samples
Download data: TXT
Series
Accession:
GSE162987
ID:
200162987
17.

Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur Without Genome Modifications

(Submitter supplied) Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. more...
Organism:
Saccharomyces cerevisiae; Saccharomyces cerevisiae W303
Type:
Expression profiling by array
Platform:
GPL22543
3 Samples
Download data: TXT, XLSX
Series
Accession:
GSE162203
ID:
200162203
18.

Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress

(Submitter supplied) In this study, we elucidate the common logic of the RPGs regulatory network by evaluating both the architecture and activity of promoters under conditions of stress or modulation of TF levels, and we identified the proteins regulating the activity of promoters lacking Rap1 binding, thus demonstrating that RPG co-regulation requires the complementary action of two different mechanisms involving both Ifh1 and Sfp1.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL17342
22 Samples
Download data: BIGWIG, BW
19.

Transcriptomic analysis of osmotic stress response in yeast xrn1 mutant

(Submitter supplied) The goal of the project was to study the response in transcription rates after 0.6M KCl addition genome wide. We used Genomic Run-On (GRO) experiment taking samples at 0, 8, 15, 30, and 45 minutes after salt addition in wild type and xrn1 mutant strains.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL24365
10 Samples
Download data: TXT
Series
Accession:
GSE151736
ID:
200151736
20.

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae

(Submitter supplied) Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL19756
18 Samples
Download data: BEDGRAPH
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