GEO DataSets

(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

(Submitter supplied) Transcriptome analysis was performed to identify the differentially expressed genes between hapX mutant and reference strains during their growth on maltose

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21721

4 Samples

Download data: XLS

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28173

12 Samples

Download data: BW

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Kluyveromyces lactis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34174

16 Samples

Download data: BW

(Submitter supplied) Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Other

Platform:

GPL28173

50 Samples

Download data: BW

(Submitter supplied) Aspergillus niger fulfills an important role in nature in nutrient cycling and is a main cell factory for the industrial production of metabolites and enzymes. Inactivation of flbA in A. niger results in thinner cell walls, increased cell lysis, abolished sporulation, and an increased secretome complexity. A total of 36 transcription factor genes are differentially expressed in ∆flbA. Here, seven of these genes (abaA, aslA, aslB, azf1, htfA, nosA, and srbA) were inactivated. more...

Organism:

Aspergillus niger

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34135

9 Samples

Download data: TSV, XLSX

(Submitter supplied) RNA-seq on total RNA of wild type (WT) and set2 mutant (set2d). To determine the changes in transcriptome profile when set2 gene is delete in comparision to WT cells.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13988

4 Samples

Download data: TXT

(Submitter supplied) Our characterization of Mug174 using genetic and biochemical approaches revealed that Mug174 is the Coilin (an integral component of the Cajal body in multicellular organisms) ortholog in the fission yeast S. pombe. To investigate the Mug174 role in shaping transcriptome, we delete the mug174 gene and performed RNA-seq. We found that intron and exon-intron junction reads were elevated in mug174∆, indicating that pre-mRNA splicing is compromised in the absence of Mug174. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30067

6 Samples

Download data: XLS

(Submitter supplied) The goal of this study was to test the effect of metal cations (CaCl2 and MnCl2) during Pol II NET-seq. These metals are readily used in the majority of studies that use NET-seq to analyze Pol II occupancy, but their effect on nascent transcript capture has not been analyzed. Our results suggest that the inclusion of these metals in Pol II NET-seq experiments does not cause a significant change in Pol II occupancy in the untreated control vs. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL27812

9 Samples

Download data: BW

(Submitter supplied) Candida auris has emerged as a significant healthcare-associated pathogen, posing a serious challenge due to its multidrug-resistant nature. Given the pre-existing constraints in the discovery and provision of new antifungals, there is thus an urgent imperative to design effective strategies to tackle this pressing global concern. Here, we screened a chemical library and identified phenyl-carbohydrazide derivatives with potent activity against both C. more...

Organism:

Candida albicans SC5314; [Candida] auris

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL33190 GPL34459 GPL28368

24 Samples

Download data: TXT

(Submitter supplied) Protein folding is driven by the burial of hydrophobic amino acids in a tightly-packed core that excludes water. The genetics, biophysics and evolution of hydrophobic cores are not well understood, in part because of a lack of systematic experimental data on sequence combinations that do - and do not - constitute stable and functional cores. Here we randomize protein hydrophobic cores and evaluate their stability and function at scale. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL19756 GPL31112

16 Samples

Download data: CSV

(Submitter supplied) Although most known mycoviruses are asymptomatic or reduce the virulence of their host fungi, those that confer hypervirulence to entomopathogenic fungus still need to be explored. Here, we discovered and studied a novel mycovirus in Metarhizium flavoviride, isolated from Laodelphax striatellus. Based on molecular analysis, we tentatively designated the mycovirus as Metarhizium flavoviride partitivirus 1 (MfPV1), a novel species in genus Gammapartitivirus, family Partitiviridae. more...

Organism:

Metarhizium anisopliae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34433

6 Samples

Download data: TXT

(Submitter supplied) Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. more...

Organism:

Escherichia coli; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL21222 GPL17342

19 Samples

Download data: TXT

(Submitter supplied) Reprogramming a non-methylotrophic industrial host, such as Saccharomyces cerevisiae, to a synthetic methylotroph reprents a huge challenge due to the complex regulation in yeast. Through TMC strategy together with ALE strategy, we completed a strict synthetic methylotrophic yeast that could use methanol as the sole carbon source. However, how cells respond to methanol and remodel cellular metabolic network on methanol were not clear. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

6 Samples

Download data: CSV

(Submitter supplied) Fungal necromass in soil represents the stable carbon pools. While fungi are known to decompose fungal necromass, how fungi decomopose melanin, remains poorly understood. Recently, Trichoderma species was found to be one of the most commonly associated fungi in soil, we have used a relevant fungal species, Trichoderma reesei, to characterized Genes involved in the decomposition of melanized and non-melanized necromass from Hyaloscypha bicolor.

Organism:

Trichoderma reesei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34370

9 Samples

Download data: CSV

(Submitter supplied) Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

5 Samples

Download data: BW

(Submitter supplied) Aneuploidy has a myriad of consequences for health and disease, yet models of aneuploidy toxicity are still widely debated. To distinguish the effects of specific genes from the generalized burden of chromosome amplification, we measured the effects of duplicating individual genes in euploid cells as well as in select aneuploids using a barcoded plasmid library. We analyzed the responses of cells with and without extra chromosomes, as well as those with and without RNA-binding protein Ssd1. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

83 Samples

Download data: CSV

(Submitter supplied) Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28475

6 Samples

Download data: CSV

(Submitter supplied) We report on how the absence of expansion segment 7S from the yeast ribosome alters A-site occupancy along transcripts. This has consequence for local translation rates and protein fidelity.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

11 Samples

Download data: TXT