GEO DataSets

(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

(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

(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

(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

(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

(Submitter supplied) SPT5 is a well-conserved factor which manipulates multiple stages of transcription including promoter-proximal pausing (PPP). Furthermore, recent studies have reported an unidentified increase of antisesne transcripts near promoters in SPT5 mutations. Here, we have identified Spt5p-restricted intragenic antisense transcripts which are in close relationship with sense transcription. The antisense highly-restricted genes have common properties: endogenously strong sense transcription and weak antisense transcription, which is also conserved in humans. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26171 GPL27812

76 Samples

Download data: BW

(Submitter supplied) SPT5 is a well-conserved factor which manipulates multiple stages of transcription including promoter-proximal pausing (PPP). Furthermore, recent studies have reported an unidentified increase of antisesne transcripts near promoters in SPT5 mutations. Here, we have identified Spt5p-restricted intragenic antisense transcripts which are in close relationship with sense transcription. The antisense highly-restricted genes have common properties: endogenously strong sense transcription and weak antisense transcription, which is also conserved in humans. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26171

24 Samples

Download data: BW

(Submitter supplied) SPT5 is a well-conserved factor which manipulates multiple stages of transcription including promoter-proximal pausing (PPP). Furthermore, recent studies have reported an unidentified increase of antisesne transcripts near promoters in SPT5 mutations. Here, we have identified Spt5p-restricted intragenic antisense transcripts which are in close relationship with sense transcription. The antisense highly-restricted genes have common properties: endogenously strong sense transcription and weak antisense transcription, which is also conserved in humans. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26171

49 Samples

Download data: BW

(Submitter supplied) Gene expression was quantified in S. cerevisiae cells after 40 hours of LiCl treatment or control conditions. Cells expressing wild type (WT) Hcm1, a stable Hcm1 mutant (Hcm1-3N), or a consitutitvely active, phosphomimetic mutant (Hcm1-8E) were compared to allow the identification of genes whose expression depends upon dynamic phosphorylation of Hcm1. We found that dynamic phosphorylation of Hcm1 is required for expression of Hcm1 target genes in LiCl stress.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30266

18 Samples

Download data: CSV

(Submitter supplied) In eukaryotes, the hetero-hexameric origin recognition complex (ORC) is responsible for assembling Mcm2-7 complex into a head-to-head double hexamer (DH), forming pre-replicative complex (pre-RC) that licenses origin DNA for replication initiation. This process is tightly controlled throughout the cell cycle to ensure accurate duplication of the genome. Here we show that the N-terminal intrinsically disordered region (IDR) of the yeast Orc2 subunit plays a critical role in promoting pre-RC assembly. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL34342

6 Samples

Download data: BED

(Submitter supplied) To investigate the functionality of sequences as transcription activation domains (TADs), a library was screened for growth on aureobasidin-containing growth media. Libraries of designed sequences were investigated to identify certain features associated with TAD functionality, such as balance between acidic and aromatic amino acids, and preferential location of certain types of amino acids.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

6 Samples

Download data: FA, FASTA, TAB, TXT

(Submitter supplied) Dynamic 3' UTRs variation mediated by APA is one of the major determinants of post-transcriptional regulation. Though some progress has been made in understanding its function in mammalian cells, the role of APA in the model organism S. cerevisiae, which lack of miRNAs, is a matter of debate. Unlike mammalian cells, most of S. cerevisiae genes tend to express mRNAs with longer 3′ UTRs in proliferating cells. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL26171

18 Samples

Download data: TXT

(Submitter supplied) Coenzyme Q (CoQ) is a redox-active lipid molecule that acts as an electron carrier in the mitochondrial electron transport chain. In Saccharomyces cerevisiae, CoQ is synthesized in the mitochondrial matrix by a multi-subunit protein-lipid complex termed the CoQ synthome, the spatial positioning of which is coordinated by the Endoplasmic Reticulum-Mitochondria Encounter Structure (ERMES). The MDM12 gene encoding the cytosolic subunit of ERMES, MDM12, is co-expressed with COQ10, which encodes the putative CoQ chaperone Coq10, via a shared bidirectional promoter. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25739

12 Samples

Download data: CSV

(Submitter supplied) WT and N88S seipin-expressing cells were grown in SC-glucose medium to exponential phase and then iron chelator bathophenanthrolinedisulfonate (BPS) was added to a final concentration of 100 micromolar. Cells were incubated in the presence of BPS for an additional 4 hour period. We intend to evaluate differentially expressed genes (DEGs) between the two strains. Four biological replicates (classified as 1-4 for the corresponding strain) were used per strain.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33987

8 Samples

Download data: TXT

(Submitter supplied) Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

36 Samples

Download data: TXT

(Submitter supplied) The prevailing model postulates that complete cytoplasmic polyadenosine tail (pA-tail) deadenylation is essential for initiating mRNA decapping and subsequent degradation. To investigate this, we conducted direct RNA sequencing of yeast mRNAs derived from steady-state and stress condition chase experiments. Subsequently, we developed a numerical model based on a modified gamma distribution function, which estimated the transcriptomic deadenylation rate at 10 A/min. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25739

94 Samples

Download data: CSV

(Submitter supplied) During the application of thermal treatment, cell survival depends on biological factors (such as growth stage, culture conditions, and the composition of the stress medium) as well as physical factors inherent to the thermal process (including amplitude, duration at the stress temperature, and the rate of temperature increase). In this study, the yeast Saccharomyces cerevisiae BY4742 was exposed to two different thermal treatment kinetics in a nutrient medium after being cultivated in YPD medium at 25 °C for 48 hours (to reach the stationary growth phase). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17582

9 Samples

Download data: TXT

(Submitter supplied) The SWR1 chromatin remodeling complex (SRCAP in humans) is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here we use cryo-EM to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

9 Samples

Download data: BW

(Submitter supplied) Chemical RNA modifications, collectively referred to as the ‘epitranscriptome’, have been intensively studied during the last years, largely facilitated by the use of next-generation sequencing technologies. Recent efforts have turned towards the nanopore direct RNA sequencing (DRS) platform, as it allows simultaneous detection of diverse RNA modification types in full-length native RNA molecules. While RNA modifications can be identified in the form of systematic basecalling ‘errors’ in DRS datasets, m6A modifications produce very modest ‘errors’, limiting the applicability of this approach to sites that are modified at high stoichiometries. more...

Organism:

Arabidopsis thaliana; Homo sapiens; Mus musculus; Saccharomyces cerevisiae; synthetic construct; Xenopus laevis

Type:

Other

6 related Platforms

70 Samples

Download data: CSV, FA, FASTA, TSV, TXT

(Submitter supplied) The relationship between aging and RNA biogenesis and trafficking is attracting growing interest, yet the precise mechanisms are unknown. The THO complex is crucial for mRNA cotranscriptional maturation and export. Herein, we report that the THO complex is closely linked to maintaining a normal lifespan. Deficiencies in Hpr1 and Tho2, components of the THO complex, reduced replicative lifespan (RLS) and are linked to a novel Sir2-independent RLS control pathway. more...

Organism:

Saccharomyces cerevisiae S288C

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33992

4 Samples

Download data: XLSX