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Items: 1 to 20 of 3865

1.

Acetylation-dependent Multimerization of SAGA Regulates Gene Transcription

(Submitter supplied) In Saccharomyces cerevisiae, the SAGA complex regulates its own activity by undergoing multimerization. This multimerization is triggered by SAGA autoacetylation at three sites on its Ada3 subunit, allowing recognition of this acetylation by the bromodomain of the Gcn5/Spt7 SAGA subunit. Once multimerized, SAGA is capable of cooperatively acetylating chromatin, and an inability to autoacetylate Ada3 leads to transcriptional and phenotypic defects in a wide range of stress-activated genes. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
30 Samples
Download data: TXT
Series
Accession:
GSE161887
ID:
200161887
2.

A stress-induced error prone 3' flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL17342
17 Samples
Download data: TXT
Series
Accession:
GSE178876
ID:
200178876
3.

A stress-induced error prone 3’ flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival (WGS)

(Submitter supplied) Faithful and efficient Okazaki fragment maturation is the key to maintain the genome integrity. In addition, this process is coupled with deposition of histone proteins. Therefore, functional deficiency in Okazaki fragment maturation may cause genome instablities as well and epigenetic alterations. We conduct WGS of WT and rad27 knockout yeast strains to define the DNA mutations caused by defective Okazaki fragment muturaton and conduct RNA-seq to define the changes in gene expression profiling due to defetive Okazaki fragment muturations..
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
9 Samples
Download data: TXT
Series
Accession:
GSE178875
ID:
200178875
4.

A stress-induced error prone 3’ flap-based Okazaki fragment maturation pathway creates internal tandem duplications for cell survival (RNA-seq)

(Submitter supplied) Faithful and efficient Okazaki fragment maturation is the key to maintain the genome integrity. In addition, this process is coupled with deposition of histone proteins. Therefore, functional deficiency in Okazaki fragment maturation may cause genome instablities as well and epigenetic alterations. We conduct WGS of WT and rad27 knockout yeast strains to define the DNA mutations caused by defective Okazaki fragment muturaton and conduct RNA-seq to define the changes in gene expression profiling due to defetive Okazaki fragment muturations..
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
8 Samples
Download data: TXT
Series
Accession:
GSE178873
ID:
200178873
5.

Mechanism of nucleosome positioning, spacing and regularity in Saccharomyces cerevisiae

(Submitter supplied) Numerous nucleosome remodeling enzymes tightly regulate nucleosome positions in eukaryotic cells. Transcription and statistical positioning of nucleosomes may also contribute to proper nucleosome organization. Individual contributions remain controversial due to strong redundancy of processes acting on the nucleosome landscape. By incisive yeast genome engineering we radically decreased their redundancy. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18085
95 Samples
Download data: BW
Series
Accession:
GSE141007
ID:
200141007
6.

Gene expression analysis of yeast lacking Set4 under normal and stress conditions

(Submitter supplied) Genome-wide gene expression data were generated for wildtype and set4 mutant yeast under aerobic and hypoxic conditions to determine the contribution of Set4 to gene expression. Illumina-based sequencing was performed on strand-specific libraries prepared from mRNA purified from yeast grown in rich medium aerobically or under hypoxia. Reads were processed for qualiy control, mapped to the genome, and differential gene expression was determined based on log fold-change differences between set4 mutants and wildtype.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
12 Samples
Download data: XLSX
Series
Accession:
GSE173901
ID:
200173901
7.

Adaptive local false discovery rate procedures for highly spiky data and their application to RNA sequencing data of yeast SET4 deletion mutants

(Submitter supplied) Genome-wide gene expression data were genertated for wildtype and set4 mutant yeast to determine the contribution of Set4 to gene expression under standard growth conditions. Illumina-based sequencing was performed on strand-specific libraries prepared from mRNA purified from yeast under standard (YPD-rich medium, no stress) growth conditions. Reads were procesed for qualiy control, mapped to the genome, and differential gene expression was determined using based on log fold-change difference between set4 mutants and wildtype. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
6 Samples
Download data: XLS
Series
Accession:
GSE173653
ID:
200173653
8.

ChIP-seq facilitates the quantitative analysis of Rvb proteins' enrichment on the genome during stress

(Submitter supplied) The goals of this study are to quantitatively analyze the enrichment of Rvb1/Rvb2 on the yeast genome during glucose starvation. The ChIP-seq files were generated from 2 biological replicates of Rvb1’s immunoprecipitation (IP), Rvb2-IP, and Pgk1-IP in 10-min glucose starved yeast cells, respectively, using NextSeq 500 SR 75. The sequence reads that passed quality filters were analyzed by calculation of the read counts on 2 regions: -500 bp to TSS and TSS to +500 bp. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
9 Samples
Download data: CSV
Series
Accession:
GSE184473
ID:
200184473
9.

Genome-wide localization of SUMO-modified proteins in untreated or heat-shocked budding yeast

(Submitter supplied) Most SUMO-modified proteins in budding yeast and human cells are associated with chromatin. To determine specifically where sumoylated proteins are found across the genome, we performed ChIP-seq with a SUMO antibody in budding yeast. We identified 603 loci that each contain a stable SUMO peak. In agreement with a previous study, most of these sites correspond to tRNA genes or genes that encode ribosomal proteins (RPGs). more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
12 Samples
Download data: NARROWPEAK
Series
Accession:
GSE167425
ID:
200167425
10.

A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Other; Genome variation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19756 GPL27812 GPL21656
16 Samples
Download data: BW, TXT
Series
Accession:
GSE180167
ID:
200180167
11.

A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress [ChIP-seq]

(Submitter supplied) Upon replication stress, the Mec1ATR kinase triggers the downregulation of transcription, reducing the level of RNA polymerase on chromatin to facilitate replication fork progression. We identify a hydroxyurea-induced phosphorylation site at Mec1-S1991 that contributes to the eviction of RNAPII and RNAPIII during replication stress. The non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL19756 GPL27812
8 Samples
Download data: TXT
Series
Accession:
GSE180165
ID:
200180165
12.

A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress [copy_number]

(Submitter supplied) Upon replication stress, the Mec1ATR kinase triggers the downregulation of transcription, reducing the level of RNA polymerase on chromatin to facilitate replication fork progression. We identify a hydroxyurea-induced phosphorylation site at Mec1-S1991 that contributes to the eviction of RNAPII and RNAPIII during replication stress. The non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by high throughput sequencing
Platform:
GPL21656
4 Samples
Download data: BW
Series
Accession:
GSE180164
ID:
200180164
13.

A regulatory phosphosite on Mec1 controls RNAPII and RNAPIII occupancy during replication stress [tDNA]

(Submitter supplied) Upon replication stress, the Mec1ATR kinase triggers the downregulation of transcription, reducing the level of RNA polymerase on chromatin to facilitate replication fork progression. We identify a hydroxyurea-induced phosphorylation site at Mec1-S1991 that contributes to the eviction of RNAPII and RNAPIII during replication stress. The non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. more...
Organism:
Saccharomyces cerevisiae
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19756
4 Samples
Download data: CSV
Series
Accession:
GSE179791
ID:
200179791
14.

Adaptive evolution under modest thermal stress improves the thermotolerance and ethanol fermentability of Saccharomyces cerevisiae

(Submitter supplied) Thermotolerance development of robust Saccharomyces cerevisiae is necessary to enhance enzyme activity of cellulase, lower cooling costs, and reduce cell harm from the bad-distributed heat transfer in large-scale fermentation. The process-based studies of adaptive evolution have been well documented, but it remains unknown for the underlying molecular mechanism of the improved thermotolerance and the facilitated ethanol fermentability derived from adaptive evolution. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
10 Samples
Download data: XLSX
Series
Accession:
GSE182342
ID:
200182342
15.

Specialized ribosomes in yeast as a response to oxidative stress

(Submitter supplied) The yeast genome contains a substantial amount of duplicated ribosomal protein genes. Functional characterization of deletion strains of individual paralogs show that the phenotypes upon deletion are not the same for a given paralog pair, suggesting that ribosomal protein paralog genes have distinct functions and thus are not redundant. Here we aimed to explore the differential function of RPL22A and RPL22B in protein synthesis. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
24 Samples
Download data: TSV
Series
Accession:
GSE118296
ID:
200118296
16.

A mechanism of coupling leading and lagging strand DNA synthesis under replication stress in budding yeast

(Submitter supplied) Here we show that the asymmetric DNA synthesis is also observed in mec1-100 and mrc1-AQ cells defective in replication checkpoint, but surprisingly, not in mrc1∆ cells in which both DNA replication and checkpoint functions of Mrc1 are missing. Furthermore, depletion of Mrc1 or its partner in DNA replication, Tof1, suppresses the asymmetric DNA synthesis in rad53-1 mutant cells.
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
Platform:
GPL13821
36 Samples
Download data: BW
Series
Accession:
GSE172093
ID:
200172093
17.

Base editing of general transcription factor Spt15 to enhance yeast stress tolerance

(Submitter supplied) We aimed to explore the application of the Target-AID base editor in genomic in situ protein engineering by generating nonsynonymous mutations. A general transcription factor Spt15 (TATA-box binding protein) gene of Saccharomyces cerevisiae was selected as a target. Based on computational and experimental scanning mutagenesis of the Spt15 gene as well as flask-fermentation screening, three stress-tolerant Spt15 mutant strains (A140G, P169A and R238K) and two stress-sensitive Spt15 mutant strains (S118L and L214V) were obtained. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
34 Samples
Download data: TXT
Series
Accession:
GSE160256
ID:
200160256
18.

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:
Homo sapiens; Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20276
8 Samples
Download data: BIGWIG
Series
Accession:
GSE178213
ID:
200178213
19.

Spo11 generates gaps through concerted cuts at sites of topological stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces kudriavzevii; Saccharomyces cerevisiae; [Candida] glabrata
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
20.

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
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