GEO DataSets

(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:

Saccharomyces cerevisiae; Escherichia coli

Type:

Other

Platforms:

GPL17342 GPL21222

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

(Submitter supplied) Pre-mRNA splicing is vital for the proper function and regulation of eukaryotic gene expression. Saccharomyces cerevisiae has been used as a model organism for studies of RNA splicing because of the striking conservation of the spliceosome and its catalytic activity. Nonetheless, there are relatively few annotated alternative splice forms, particularly when compared to higher eukaryotes. Here, we describe a method to combine large scale RNA sequencing data to accurately discover novel splice isoforms in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

12 Samples

Download data: TXT

(Submitter supplied) mRNAs are transcribed and processed in the nucleus before they are exported into the cytoplasm for translation. Export is mediated by the export receptor heterodimer Mex67-Mtr2 in yeast (TAP-p15 in humans). Interestingly, also many lncRNAs leave the nucleus but it is currently unclear why they travel into the cytoplasm. Here we show that antisense (as)RNAs accelerate mRNA export by annealing with their sense counterparts through the helicase Dbp2. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

6 Samples

Download data: TXT

(Submitter supplied) mRNAs are transcribed and processed in the nucleus before they are exported into the cytoplasm for translation. Export is mediated by the export receptor heterodimer Mex67-Mtr2 in yeast (TAP-p10 in humans). Interestingly, also long non-coding RNAs (lncRNAs) leave the nucleus and so-called XUTs (Xrn1 sensitive unstable transcripts) accumulate in the cytoplasm of the degradation defective xrn1∆ mutant. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

12 Samples

Download data: GTF, TXT

(Submitter supplied) We explored transcriptional responses of the fission yeast to DNA damage. RNA-seq was used to characterize changes in expression profiles of all known lncRNAs and mRNAs in wild type cells and cells treated by four DNA damage agents: Camptothecin, Hydroxyurea, Methyl methanesulfonate and Phleomycin.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

10 Samples

Download data: TXT

(Submitter supplied) Missense variants that change the amino acid sequences of proteins cause one third of human genetic diseases. Tens of millions of missense variants exist in the current human population, with the vast majority having unknown functional consequences. Here we present the first large-scale experimental analysis of human missense variants. Using DNA synthesis and cellular selection experiments we quantify the impact of >500,000 variants on the abundance of >500 human protein domains. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL27812 GPL31112 GPL19756

78 Samples

Download data: TXT

(Submitter supplied) Enzymes catalyze the reactions of life and are the targets of nearly all small molecule drugs. Most drugs inhibit enzymes by binding to conserved active sites, causing problems of specificity and toxicity. Targeting regulatory allosteric sites can increase specificity, overcome drug resistance and tune or activate activity.However, the vast majority of enzymes have no known allosteric sites and methods do not exist to globally identify or predict them.Here we present a general and fast method to globally chart allosteric communication in enzymes and apply it to the Src protein kinase to produce the first comprehensive map of negative and positive allosteric control of enzymatic activity. more...

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Other

Platform:

GPL33934

118 Samples

Download data: TXT

(Submitter supplied) Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL27812 GPL21656

279 Samples

Download data: CSV, FASTA, GFF, GFF3, TSV

(Submitter supplied) Thousands of protein domains encoded in the human genome function by binding up to a million short linear motifs embedded in intrinsically disordered regions of other proteins. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of ‘fuzzy’ dynamic residues to affinity and specificity in protein-protein interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

32 Samples

Download data: CSV

(Submitter supplied) Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

36 Samples

Download data: TXT

(Submitter supplied) Chromatin replication is intricately intertwined with DNA replication, and the recycling of parental histones is essential for epigenetic inheritance. The transfer of parental histones to both the DNA replication leading and lagging strands involves two distinct pathways: the leading strand utilizes DNA polymerase ε subunits Dpb3/Dpb4, while the lagging strand is facilitated by the MCM helicase subunit Mcm2. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21656

61 Samples

Download data: BW

(Submitter supplied) Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors, but not in non-transcription factor proteins (e.g., chromatin regulators, coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL27812

16 Samples

Download data: CSV

(Submitter supplied) Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging DNA strands, respectively. Single Dpb3 deletion (dpb3[DELTA]) or Mcm2 mutation (mcm2-3A), which each disrupt one parental histone transfer pathway, leads to the other[prime]s predominance. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21656

92 Samples

Download data: BW