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Items: 1 to 20 of 81684

1.

Transient transcriptome sequencing (TT-Seq) and 5'P-Seq of ATP-analog sensitive Kin28 budding yeast

(Submitter supplied) Inhibition of Kin28/CDK7, the kinase subunit of TFIIH, leads to defects in transcription of protein-coding genes. Despite a severe reduction in nascent RNA synthesis, the majority of mRNAs retain their steady-state level upon inhibition. In this study, we examined the determinants of mRNA stability in cells experiencing transcriptional crisis via irreversible chemical inhibition of Kin28. We discovered that the inhibited Kin28 transcriptome resembles the transcriptome of cells treated with an inhibitor of protein synthesis. more...
Organism:
Saccharomyces cerevisiae BY4741
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20138 GPL18330
24 Samples
Download data: BIGWIG
Series
Accession:
GSE125409
ID:
200125409
2.

Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [II]

(Submitter supplied) The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. For the following datasets, we created a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII. We mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL25739
29 Samples
Download data: BED, SQLITE
Series
Accession:
GSE190136
ID:
200190136
3.

Peroxisome function relies on organelle-associated mRNA translation

(Submitter supplied) Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL21656
8 Samples
Download data: TXT
Series
Accession:
GSE113567
ID:
200113567
4.

eIF3 and its mRNA-entry-channel arm contribute to the recruitment of mRNAs with long 5'-untranslated regions

(Submitter supplied) Translation initiation in eukaryotes is multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17342
16 Samples
Download data: CSV
Series
Accession:
GSE190601
ID:
200190601
5.

Expression data from parental and evolved Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration and lignocellulose-derived inhibitors

(Submitter supplied) Increasing yeast robustness against biomass-derived inhibitors and insoluble solids is essential for the realization of a bio-based economy. The xylose-fermenting Saccharomyces cereivisiae F12 strain was subjected to an adaptive laboratory evolution experiment in the presence of these stressors. The resulting evolved strain exhibit better fermentation performance in terms of xylose consumption and ethanol yields than the parental strain. more...
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL2529
6 Samples
Download data: CEL, TXT
Series
Accession:
GSE159167
ID:
200159167
6.

Expression data from Saccharomyces cerevisiae

(Submitter supplied) Saccharomyces cerevisiae is an excellent microorganism for industrial succinic acid production, but high succinic acid concentration will inhibit the growth of Saccharomyces cerevisiae then reduce the production of succinic acid. Through analysis the transcriptomic data of Saccharomyces cerevisiae with different genetic backgrounds under different succinic acid stress, we hope to find the response mechanism of Saccharomyces cerevisiae to succinic acid.
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL2529
9 Samples
Download data: CEL
Series
Accession:
GSE193190
ID:
200193190
7.

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
8.

Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes

(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
Platforms:
GPL19756 GPL27812
46 Samples
Download data
Series
Accession:
GSE178161
ID:
200178161
9.

Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes [RNA-seq]

(Submitter supplied) Acetyl-CoA is a key intermediate in metabolism situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables gene expression to be coordinated with metabolic state. Previous studies have linked abundant histone acetylation to activation of genes involved in cell growth or tumorigenesis. However, under glucose starvation, the extent to which histone acetylation is important for gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19756 GPL27812
16 Samples
Download data: TXT
Series
Accession:
GSE178160
ID:
200178160
10.

Glucose Starvation Induces a Switch in the Histone Acetylome for Activation of Gluconeogenic and Fat Metabolism Genes [ChIP-seq]

(Submitter supplied) Acetyl-CoA is a key intermediate in metabolism situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables gene expression to be coordinated with metabolic state. Previous studies have linked abundant histone acetylation to activation of genes involved in cell growth or tumorigenesis. However, under glucose starvation, the extent to which histone acetylation is important for gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
30 Samples
Download data: BW
Series
Accession:
GSE178159
ID:
200178159
11.

Time series data of chromatin and transcription throughout the cell cycle

(Submitter supplied) The occupancy states of DNA-binding nucleosomes and subnucleosome-sized proteins (e.g.  transcription factors, replication proteins, etc.) determine the chromatin accessibility landscape and provide additional regulatory context for DNA-templated processes including transcription and DNA replication. Throughout the mitotic cell division cycles, the transcriptome undergoes periodic reprogramming along with replication- and mitosis-induced global chromatin reconfiguration; however, profiling of the cell cycle-specific chromatin dynamics and understandings of its regulatory mechanisms remain limited. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
59 Samples
Download data: CSV
Series
Accession:
GSE168699
ID:
200168699
12.

Functional characterization of the transcription programs underlying phase transition in the BSL3 pathogen Coccidioides immitis

(Submitter supplied) Coccidioidomycosis (Valley Fever) is an emerging endemic fungal infection with a rising incidence and an expanding geographic range. It is caused by Coccidiodes, which are thermally dimorphic fungi that grow as mycelia in soil but transition in the lung to form pathogenic spherules. The regulatory mechanisms underlying this transition are not understood. Exploiting capped small (cs)RNA-seq, which identifies actively initiated stable and unstable transcripts and thereby detects acute changes in gene regulation with remarkable sensitivity, here we report the changes in architectural organization and key sequence features underlying phase transition of this highly pathogenic fungus. more...
Organism:
Schizosaccharomyces pombe; Agaricus bisporus; Coccidioides immitis; Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
7 related Platforms
27 Samples
Download data: GTF, TXT
Series
Accession:
GSE179468
ID:
200179468
13.

A hexasome is the preferred substrate for the INO80 chromatin remodeling complex allowing versatility of function

(Submitter supplied) The INO80 chromatin remodeling complex plays critical roles in transcription that are commonly attributed to INO80’s nucleosome sliding activity. Here we find that removal of INO80 in yeast cells disrupts the positions of hexasome-sized particles within genes. We show that in vitro INO80 remodels hexasomes ~60-fold faster than nucleosomes. INO80’s preference for hexasomes is highest when the linker lengths approach the ~18 bp linker lengths found in gene bodies. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26302
4 Samples
Download data: BAM
Series
Accession:
GSE168700
ID:
200168700
14.

Stress-driven feedback regulation of multiple tolerant genes improves xylose fermentation of Saccharomyces cerevisiae

(Submitter supplied) The modification of the The modification of the tolerance of xylose-fermenting yeast is an urgent issue for improving ethanol production. In this study, multiple genes involving in superoxide dismutase, glutathione biosynthesis, NADPH regeneration and acetic acid degradation were overexpressed using stress-induced promoters, which is selected from the transcriptome data. Stress-induced promoters were used to realize the feedback control of the tolerant genes, which can ultimately improve the tolerance and ethanol production. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25927
4 Samples
Download data: CSV
Series
Accession:
GSE140075
ID:
200140075
15.

Analysis of alkylation damage formation and base excision repair at yeast transcription factor binding sites

(Submitter supplied) DNA base damage arises frequently in all living cells and is an important contributor to mutations and genome instability. The main repair pathway for base damage is base excision repair (BER). How the formation and repair of base lesions are modulated by DNA-binding proteins is poorly understood. Here we used a high-throughput damage mapping method, N-methylpurine-sequencing (NMP-seq), to characterize alkylation damage distribution and BER at yeast transcription factor (TF) binding sites upon the treatment with alkylating agent methyl methanesulfonate (MMS). more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL18249
12 Samples
Download data: WIG
Series
Accession:
GSE183622
ID:
200183622
16.

The DNA polymerase subunit Pol32 and RNase H1 are required for stress granule formation through R-loop regulation

(Submitter supplied) Strong cellular stress causes wide-spread perturbations in the transcriptome and in several types of DNA/RNA interactions, and through incompletely understood pathways to formation of cytoplasmic stress granules (SGs). We have investigated the relationships between strong transcriptional induction, RNA:DNA hybrid stretches (R-loops), and SG formation under severe hyperosmotic and glucose stress. Several mutations affecting DNA processing proteins, including the DNA polymerase subunit Pol32, confer SG formation defects. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13821
10 Samples
Download data: CSV
Series
Accession:
GSE122423
ID:
200122423
17.

Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly

(Submitter supplied) ATP-dependent chromatin remodelers (CRs), including SWI/SNF, RSC and Ino80C in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently by evicting nucleosomes from the Gcn4 binding motifs.  At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL23014
71 Samples
Download data: BW
Series
Accession:
GSE192592
ID:
200192592
18.

Genome-Scale Patterns in The Loss of Heterozygosity Incidence in Saccharomyces cerevisiae

(Submitter supplied) We applied extensive assays--repeated over several genetic backgrounds and environments--to reveal some general features of the loss of heterozygosity (LOH) in yeast. We found that LOH: was most frequent in homozygotes, was more densely distributed on shorter chromosomal arms, depended on the presence of some repetitive elements but not the intensity of transcription, occured also in absence of growth although at a low rate. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
12 Samples
Download data: TXT
Series
Accession:
GSE192479
ID:
200192479
19.

The evolution, evolvability, and engineering of gene regulatory DNA [RNA-seq]

(Submitter supplied) Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.
Organism:
Schizosaccharomyces pombe; [Candida] glabrata; Kluyveromyces lactis; Schizosaccharomyces japonicus; Schizosaccharomyces octosporus; Saccharomyces bayanus; Yarrowia lipolytica; Naumovozyma castellii; Lachancea waltii; Saccharomyces cerevisiae; Candida albicans
Type:
Expression profiling by high throughput sequencing
11 related Platforms
11 Samples
Download data: TXT
Series
Accession:
GSE163866
ID:
200163866
20.

The evolution, evolvability, and engineering of gene regulatory DNA [GPRA]

(Submitter supplied) In order to generate data produce a generalizable sequence-to-expression model, we randomly sampled ~21 million 80 bp sequences and tested their activity as promoters (in yeast) by measuring expression level by FACS (sorting into 18 bins).
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL19756
36 Samples
Download data: TXT
Series
Accession:
GSE163045
ID:
200163045
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