GEO DataSets

(Submitter supplied) Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. Here, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

6 Samples

Download data: CSV

(Submitter supplied) Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relation-ship between H3K9ac and gene expression remains largely correlative. In this study, we identify a large suite of growth-related genes in yeast that undergo a particularly strong down-regulation of both transcription and H3K9ac upon stress, and delineate the roles of transcriptional activa-tors, repressors, SAGA histone acetyltransferase, and RNA-polymerase II in this response. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

34 Samples

Download data: BIGWIG

(Submitter supplied) The populational variance of eukaryotic transcription differs by gene, and can be range from constitutive to bursty in nature. Exemplary bursty yeast genes tend to rely on SAGA and Mediator Tail (coactivator-redundant, CR) for transcription, and often contain TATA boxes in their promoters. To dissect gene-specific transcriptional bursting and the roles of coactivator complexes in regulating bursting in yeast, we performed genome-wide nascent single-cell RNA-seq. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31112

8 Samples

Download data: MTX, TSV

(Submitter supplied) Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have been revealed by combined structure-function analyses, structural information on an aberrant spliceosome committed to discard is not available. Here, we report the cryo-EM structure of a B state spliceosome intermediate primed for disassembly. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

3 Samples

Download data: BW

(Submitter supplied) Profiling of Gln3 IDR sequence to reveal specificity determinants and their regulation

Organism:

Saccharomyces cerevisiae

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

327 Samples

Download data: TXT

(Submitter supplied) The main decay pathway of yeast mRNAs in the cytoplasm uses the 5’-3’ exonuclease Xrn1. This protein shuttles from the cytoplasm to the nucleus, where it has a role as transcription factor. We have recently demonstrated that importing depends on two nuclear localization sequences (NLS 1 & NLS2) and that exporting depends on its binding (presumably co-transcriptional) to mRNAs. It is also known that Xrn1 is able to degrade decapped mRNAs that are still being translated by ribosomes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL24366

8 Samples

Download data: TXT

(Submitter supplied) Beauveria bassiana is a popular and eco-friendly biopesticide. Sensing N-acetylglucosamine (GlcNAc) , a building block of both insect exoskeleton and fungal cell wall, might play a vital role during B. bassiana pathogen-pest interaction. Previous studies in Candida albicans have demonstrated that a GlcNAc sensor (termed as Ngs1) was in response to GlcNAc signal sensing and transportation. Herein, we found a Ngs1 homology in B. more...

Organism:

Beauveria bassiana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16038

6 Samples

Download data: TXT, XLS

(Submitter supplied) H3K4 methylation is a conserved histone modification crucial for gene regulation, yet the post-translational modifications of the Set1-COMPASS complex remain largely unexplored. This study elucidates the significance of N-terminal acetylation in modulating H3K4 methylation patterns. Firstly, loss of NatA complex resulted in a significant decrease in H3K4me3 levels and a shift of H3K4me2 from 5' transcribed regions to promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17143

10 Samples

Download data: BW

(Submitter supplied) Transcription coupled-nucleotide excision repair (TC-NER) repairs DNA lesions that stall RNA polymerase II (Pol II) transcription. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD is required for efficient Rad26-dependent and Rad26-independent TC-NER across the yeast genome. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL27831 GPL18249

16 Samples

Download data: TXT, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL21656 GPL17143

46 Samples

Download data: BW

(Submitter supplied) H3K4 methylation is a conserved histone modification crucial for gene regulation, yet the post-translational modifications of the Set1-COMPASS complex remain largely unexplored. This study elucidates the significance of N-terminal acetylation in modulating H3K4 methylation patterns. Firstly, loss of NatA complex resulted in a significant decrease in H3K4me3 levels and a shift of H3K4me2 from 5' transcribed regions to promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21656

12 Samples

Download data: BW

(Submitter supplied) H3K4 methylation is a conserved histone modification crucial for gene regulation, yet the post-translational modifications of the Set1-COMPASS complex remain largely unexplored. This study elucidates the significance of N-terminal acetylation in modulating H3K4 methylation patterns. Firstly, loss of NatA complex resulted in a significant decrease in H3K4me3 levels and a shift of H3K4me2 from 5' transcribed regions to promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: BW

(Submitter supplied) How parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications, are transferred to leading and lagging strands of DNA replication forks following DNA replication is an important question that remains not well understood. Here we show that DNA polymerase clamp PCNA and its partner involved in lagging strand DNA synthesis, Pol d, regulate parental histone transfer to lagging strands. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

274 Samples

Download data

(Submitter supplied) At human body temperature, the fungal pathogen Candida albicans can transition from yeast to filamentous morphologies in response to host-relevant cues. Additionally, elevated temperatures encountered during febrile episodes can independently induce C. albicans filamentation. However, the underlying genetic pathways governing this developmental transition in response to elevated temperature remain largely unexplored. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28323

21 Samples

Download data: TDF, TXT

(Submitter supplied) The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. more...

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL33056

36 Samples

Download data: CSV

(Submitter supplied) Aspergillus fumigatus is an important human pathogen and a leading fungal killer. This study aimed to determine the tRNA fragment and tRNA half repertoire of A. fumigatus in wild-type conidia and mycelium grown for 24 or 48 hours in liquid culture.

Organism:

Aspergillus fumigatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23268

9 Samples

Download data: CSV

(Submitter supplied) In yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 (SUP45) and eRF3 (SUP35), which are essential for viability. Previous studies have revealed that presence of nonsense mutations in these genes leads to amplification of mutant alleles (sup35-n and sup45-n) which appears to be necessary for viability of such cells. However, the mechanism of this phenomenon remained unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

10 Samples

Download data: TXT

(Submitter supplied) We report the ChIP-seq profiling of a transcriptional factor Sef1 in Sccharomyces cerevisiae, and show that ScSef1 targets many TCA cycle and many others genes but has very limited regulatory effects to these target genes.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

14 Samples

Download data: BIGWIG, NARROWPEAK, TXT, WIG

(Submitter supplied) Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external stimuli. We have developed several life constructs that allow the quantification of fission yeast splicing in vivo on intact cells, and we have compared their splicing efficiency in a wild type strain and in a prp2-1 (U2AF65) genetic background, showing a clear dependency between Prp2 and a consensus signal at 5’ splicing site (5’SS). more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30658

6 Samples

Download data: TXT

(Submitter supplied) Arabidopsis gene expression is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for most Arabidopsis TFs, we lack knowledge about the presence, location, and transcriptional strength of their ADs. To address this gap, we experimentally identified Arabidopsis ADs on a proteome-wide scale, finding that over half of Arabidopsis TFs carry an AD. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL27812

164 Samples

Download data: CSV