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Items: 1 to 20 of 118368

1.

Nucleosome intermediate preference of SMARCAD1 chromatin remodeler, and the structural insights

(Submitter supplied) Examination of the repositioning of nucleosome and hexasome-sized particles induced by the SMARCAD1 family proteins in cells support the hexasome-binding mode. Our findings reveal a new mode of chromatin regulation, wherein the nucleosome intermediates are specially remodeled through an ATP-dependent process.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27812
4 Samples
Download data: BW
Series
Accession:
GSE246619
ID:
200246619

2.

Loc1 RIP-chip; Niedner et al.

(Submitter supplied) Loc1 RIP-chip Experimental procedure: C-terminally TAP-tagged Loc1p from yeast S. cerevisiae was purified from 1 L of cells grown in YPD medium as previously described (Gerber et al. 2004, PLoS Biol. 2, E79). Untagged control cells (BY4741) cells served as a negative control. cDNA was synthesized from 3 μg of total RNA derived from the extract and 500 ng of affinity-isolated RNA and labeled with Cy3 and Cy5 fluorescent dyes, respectively. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL34754 GPL34753
7 Samples
Download data: GPR
Series
Accession:
GSE273374
ID:
200273374

Analyze with GEO2R

3.

Study of the cellular component-dependent functions of Xrn1

(Submitter supplied) The main cytoplasmic mRNA decay pathway in yeast uses the 5’-3’ exonuclease Xrn1 (Parker and Song, Nat Struct Mol Biol. 2004 ). This protein shuttles from the cytoplasm to the nucleus, where it has a role as transcription factor (Haimovich et al. Cell 2013). In this work, we find that most of the global phenotypes of an xrn1 mutant are partially complemented by a cytoplasmic version of the paralogous 5’-3’exonuclease Rat1 (cRat1) indicating that this 5’-3’-exonuclease has a similar enzymatic capacity as Xrn1. more...
Organism:
Saccharomyces cerevisiae BY4741
Type:
Other
Platform:
GPL20138
36 Samples
Download data: BEDGRAPH
Series
Accession:
GSE193992
ID:
200193992

4.

Genetic Insights into the Rheological Strength of Candida albicans Biofilms

(Submitter supplied) The principal opportunistic human fungal pathogen Candida albicans forms biofilms resistant to antifungal therapeutics. Biofilms are a class of soft matter with viscoelastic properties and response to flow, but little is known regarding the genes contributing to these rheological phenotypes in fungal biofilms. Here, we identify C. albicans genes with deletion phenotypes of altered biofilm viscoelasticity. more...
Organism:
Candida albicans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28323
12 Samples
Download data: XLS
Series
Accession:
GSE276413
ID:
200276413

5.

The Fork Protection Complex generates DNA topological stress induced DNA damage while ensuring full and faithful genome duplication

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL19756
92 Samples
Download data: WIG
Series
Accession:
GSE239967
ID:
200239967

6.

The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress [TrAEL-seq]

(Submitter supplied) Tof1/Timeless, protects eukaryotic cells from DNA replication stress as part of the Fork Protection Complex (FPC). Tof1 supports rapid DNA replication, fork pausing, and resolution of DNA topological stress. Here, we show that disruption of FPC function through loss of either Tof1 or Mrc1 results in DNA damage in long replicons. Despite increasing DNA damage in long replicons, loss of either Tof1 or Mrc1 concurrently reduces DNA damage in regions prone to damage caused by DNA topological stress, indicating that the rapid replication promoted by the FPC fosters completing DNA replication at the cost of increased vulnerability to DNA topological stress. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL19756
4 Samples
Download data: WIG
Series
Accession:
GSE239966
ID:
200239966

7.

The Fork Protection Complex protects long replicons from DNA damage at the cost of genome instability induced by DNA topological stress [ChIP-seq]

(Submitter supplied) Tof1/Timeless, protects eukaryotic cells from DNA replication stress as part of the Fork Protection Complex (FPC). Tof1 supports rapid DNA replication, fork pausing, and resolution of DNA topological stress. Here, we show that disruption of FPC function through loss of either Tof1 or Mrc1 results in DNA damage in long replicons. Despite increasing DNA damage in long replicons, loss of either Tof1 or Mrc1 concurrently reduces DNA damage in regions prone to damage caused by DNA topological stress, indicating that the rapid replication promoted by the FPC fosters completing DNA replication at the cost of increased vulnerability to DNA topological stress. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
88 Samples
Download data: WIG
Series
Accession:
GSE239965
ID:
200239965

8.

In vivo RNA sequencing reveals a crucial role of Fus3-Kss1 MAPKpathway in Candida glabrata pathogenicity

(Submitter supplied) Candida glabrata is an important and increasingly common pathogen of humans, particularly in immunocompromised hosts. Despite this, little is known about how this fungus causes disease. Here, we applied RNA sequencing and an in vivo invasive infection model to identify the attributes that allow this organism to infect hosts. Fungal transcriptomes show a dramatic increase in the expression of Fus3 and Kss1, two mitogen-activated protein kinases (MAPKs), during invasive infection. more...
Organism:
Nakaseomyces glabratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33483
9 Samples
Download data: TXT
Series
Accession:
GSE279281
ID:
200279281

9.

Extreme positive epistasis for fitness in monosomic yeast strains - part 2

(Submitter supplied) The loss of a single chromosome in a diploid organism halves the dosage of many genes and is usually accompanied by a substantial decrease in fitness. We asked whether this decrease simply reflects the joint damage caused by individual gene dosage deficiencies. We measured the fitness effects of single heterozygous gene deletions in yeast and combined them for each chromosome. This predicted a negative growth rate, i.e. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
4 Samples
Download data: TSV
Series
Accession:
GSE276940
ID:
200276940

10.

Extreme positive epistasis for fitness in monosomic yeast strains - part 1

(Submitter supplied) The loss of a single chromosome in a diploid organism halves the dosage of many genes and is usually accompanied by a substantial decrease in fitness. We asked whether this decrease simply reflects the joint damage caused by individual gene dosage deficiencies. We measured the fitness effects of single heterozygous gene deletions in yeast and combined them for each chromosome. This predicted a negative growth rate, i.e. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
27 Samples
Download data: TSV
Series
Accession:
GSE217944
ID:
200217944

11.

Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in nutrient-replete cells to post-transcriptionally repress starvation-induced pathways [Ribo and RNA-seq]

(Submitter supplied) Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL27812
16 Samples
Download data: TXT
Series
Accession:
GSE270790
ID:
200270790

PubMed Full text in PMC Similar studies

12.

Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in nutrient-replete cells to post-transcriptionally repress starvation-induced pathways [ChIP-seq]

(Submitter supplied) Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27812
6 Samples
Download data: CSV
Series
Accession:
GSE270789
ID:
200270789

PubMed Full text in PMC Similar studies

13.

Specific features of the transcriptomic response to nitrogen starvation in methylotrophic yeast Komagataella phaffi

(Submitter supplied) Non-conventional methylotrophic yeast Komagataella phaffii is an important production host in biotechnology and an emerging model organism. In this work, we studied K. phaffii response to nitrogen starvation during cultivation in media with methanol as the sole carbon source. The results were compared with well-established model yeast Saccharomyces cerevisiae. Some of the observed effects of nitrogen starvation in K. more...
Organism:
Komagataella phaffii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27930
6 Samples
Download data: TXT
Series
Accession:
GSE278110
ID:
200278110

14.

The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans (RNA-Seq)

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...
Organism:
Candida albicans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32241
12 Samples
Download data: TXT
Series
Accession:
GSE267941
ID:
200267941

15.

The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans (5P-Seq)

(Submitter supplied) Candida albicans is a leading cause of fungal infections in immunocompromised patients. Management of candidemia relies on a few antifungal agents, with fluconazole being first line therapy. The emergence of fluconazole-resistant strains highlights the pressing need to improve our molecular understanding of the drug response mechanisms. By sequencing the 5’P mRNA degradation intermediates, we show that co-translational mRNA decay is common in C. more...
Organism:
Candida albicans
Type:
Other
Platform:
GPL32241
28 Samples
Download data: TXT
Series
Accession:
GSE267940
ID:
200267940

16.

The Candida auris Hog1 MAP kinase is essential for the colonization of murine skin and systemic infection

(Submitter supplied) Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemic C. auris infections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is that C. auris, unlike most Candida species, displays unique skin tropism and can stay on human skin for a prolonged period. more...
Organism:
Candidozyma auris
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29671
6 Samples
Download data: TXT
Series
Accession:
GSE256470
ID:
200256470

17.

MNase-seq data in 4 modified strains of Saccharomyces cerevisiae, treated or not with 10-Phenanthroline

(Submitter supplied) We showed that the introduction of a 81bp DNA segment in phase genes leads to the generation of fuzzier nucleosome arrays, but neither to a significant change in the placement of the +1 and –last nucleosomes, nor to a coordinate sliding of nucleosomes. This suggests that irrespectively of other nucleosomes, the +1 and –last nucleosomes are placed in well-defined regions marked by sequence-dependent intrinsic and extrinsic factors, while the rest of the nucleosomes are placed based on periodicity considerations.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13821
8 Samples
Download data: GFF
Series
Accession:
GSE255857
ID:
200255857

PubMed Full text in PMC Similar studies

18.

Comprehensive analysis of human keratinocyte and opportunistic pathogenic Candida interactions

(Submitter supplied) In recent years, microbiome studies revealed that Candida species are common colonisers of the human skin. The distribution of species however varies greatly. Although C. parapsilosis is more likely to resemble skin commensals, opinions are divided, and discrepancies are present regarding C. albicans, that is also often associated with cutaneous candidiasis. Therefore, we aimed to thoroughly assess the nature of skin epithelial cell - Candida interactions. more...
Organism:
Homo sapiens; Candida albicans
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL28323
30 Samples
Download data: CSV
Series
Accession:
GSE276717
ID:
200276717

19.

The Role of Hexokinases in Epigenetic Regulation: Insights from Altered Expression of Hexokinases and Chromatin Stability

(Submitter supplied) Hexokinases (HXKs) are the key enzymes regulating glycolysis in cells. Overexpression of HXKs has been linked to numerous types of cancers and targeting HXKs has been suggested as a potential strategy of cancer therapy. How these abnormal HKs express affect epigenetics and gene expression is less understood. In this study, we artificially altered the HXKs expression level and test its impact on the parental nucleosome transfer process, a key replication coupled-epigenetic inheritance process, in yeast cells. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL27812
16 Samples
Download data: BIGWIG
Series
Accession:
GSE245005
ID:
200245005

PubMed Full text in PMC Similar studies

20.

Deciphering mRNA binding determinants of RBPs

(Submitter supplied) We created mutliple sequence mutants of several RNA binding proteins. We thenmeasured the in-vivo RNA target specificity of them and the corresponidng (and more) wild type strains using a RNA tagging approach
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
255 Samples
Download data: TXT
Series
Accession:
GSE235209
ID:
200235209

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