GEO DataSets

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

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL20705 GPL26551

23 Samples

Download data: BEDGRAPH, BIGWIG, H5, TXT

(Submitter supplied) Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

12 Samples

Download data: TXT

(Submitter supplied) Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. more...

Organism:

Neurospora crassa

Type:

Other

Platform:

GPL20705

8 Samples

Download data: H5

(Submitter supplied) Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26551

3 Samples

Download data: BEDGRAPH, BIGWIG

(Submitter supplied) Ergosterol, a pivotal constituent of the fungal cell membrane, plays a crucial role in diverse cellular activities. Fungi inherently regulate ergosterol homeostasis, a process traditionally associated with the control of a major transcription factor, like SREBP, activated in response to ergosterol depletion, regardless of which ergosterol biosynthesis step is affected. Contrary to the established paradigm, our investigation demonstrates that the inhibition of ergosterol biosynthesis at specific steps triggers distinct transcriptional responses in erg genes across fungi, including Neurospora crassa, Aspergillus fumigatus, and Fusarium verticillioides. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31176

42 Samples

Download data: TXT

(Submitter supplied) Comparative transcriptomic analysis of genes regulated during sexual development in dark and light in the wild type and the ∆ve-1 mutant.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

84 Samples

Download data: TXT

(Submitter supplied) Codon usage bias, which refers to uneven use of synonymous codons, was shown to associate with mRNA stability from yeast to human. However, the underlying molecular basis is largely unknown. With bioinformatic analyses we unexpectedly found that codon usage bias is inversely correlated to density of out-of-frame stop codons (hidden stop codon or HSC). To understand the physiological function of HSCs, we use the frequency gene of Neurospora crassa to examine the role of HSCs in circadian rhythm. more...

Organism:

Neurospora crassa

Type:

Other

Platform:

GPL16164

1 Sample

Download data: BEDGRAPH, TXT

(Submitter supplied) Codon optimality mediated decay(COMD) is a conserved phenomenon from yeast to human. Our data suggests that COMD alson exist in neurospora crass. We resort thiolutin(inhibitor for transcription) to treat cells in different time point and transcriptionally profiled them to get the landscape of transpcriptional decay profiling.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33601

8 Samples

Download data: TAB

(Submitter supplied) Filamentous fungi are one of the primary degraders of plant biomass because of their ability to produce enzymes that break down complex polysaccharides. The production of cellulolytic enzymes in fungi is dependent on transcription factors. In this article, we identified a N. crassa Zn2Cys6 transcription factor Clr5 that regulates the expression of cellulase on cellulose. N. crassa Δclr5 exhibited a significant decrease in secreted proteins (~46%), endo-glucanase (~55%), xylanase (~33%), β-glucosidase (~38%), and exocellulase (~40%) compared with the WT, while transcriptomic analysis revealed that clr5 was essential in cellulase expression. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: XLSX

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

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL23150 GPL26551

31 Samples

Download data: BEDGRAPH, BIGWIG, BW, H5

(Submitter supplied) Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL23150 GPL26551

12 Samples

Download data: H5

(Submitter supplied) Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes: in the fungus Neurospora crassa, chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures that are anchored by heterochromatic region aggregates. However, insufficient information exists on how histone post-translational modifications, including acetylation, impact genome organization. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26551

19 Samples

Download data: BEDGRAPH, BIGWIG, BW

(Submitter supplied) Circadian clocks are evolved to adapt to the daily environment changes under different conditions. The ability to maintain circadian clock functions in response to various stress and perturbations is important for organismal fitness. Here, we show that the nutrient sensing GCN2 signaling pathway is required for robust circadian clock function under amino acid starvation in Neurospora. The deletion of GCN2 pathway components disrupts rhythmic transcription of clock gene frq by suppressing WC complex binding at the frq promoter due to its reduced histone H3 acetylation levels. more...

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32914

12 Samples

Download data: XLSX

(Submitter supplied) Orphan genes have been attributed to gene duplication followed by fast divergence, horizontal gene transfer, relocation and rearrangement, and to expression of previously non-coding sequences abundant with long repeats. However, their roles are less well described and there is a lack of working hypotheses that would guide the investigation of orphan genes. For 670 Neurospora orphan genes identified in this study, over 63% form clusters that aggregate adjacent to the telomeres and are clustered with up to 61% het-like genes, which regulate self-recognition and define vegetative compatibility groups (VCGs). more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

5 Samples

Download data: CSV, TXT

(Submitter supplied) In order to explore the stress-resistance related genes that may be regulated by upf1 in Neurospora crassa, we conducted RNA-seq experiments with upf1 knockout/WT strains treated with or without 20mM H2O2, and obtained gene expression data.

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15146

12 Samples

Download data: TXT

(Submitter supplied) To identify the role of the cleavage and polyadenylation CFIm complex (NCU02152 and NCU09014) in the circadian clock, mRNA 3' End Sequencing was performed on a knockout mutant and compared to control samples. Hundreds of polyadenylation sites are affected by loss of CFIm complex activity in Neurospora crassa.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32221

4 Samples

Download data: TXT

(Submitter supplied) Post-translational modifications (PTMs) on histones have been found to play diverse functions in regulating chromatin events and gene expression. The operation of circadian clocks heavily relies on finely tuned and timely expression of the proteins comprising core oscillators. However, most studies of PTMs’ effects on circadian clocks have been conducted using static systems in which circadian clocks are rendered arrhythmic due to the essential role of PTMs on gene expression. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32780

6 Samples

Download data: BEDGRAPH

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

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL23150 GPL20660 GPL16164

20 Samples

Download data: BIGWIG, IGV, TAB, TDF, XLSX

(Submitter supplied) The recurrent mutation of histone variant H3.3 at glycine-34 (H3.3G34) defines a type of pediatric glioma. Characteristic changes to the epigenome associated with the disease are thought to be the consequence of altered methylation of the adjacent lysine-36 (K36) residue, but the complexity of this regulatory pathway in humans, combined with a multi-component disease etiology, has limited our understanding of how H3.3G34 mutations contribute to oncogenesis. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23150 GPL20660

3 Samples

Download data: TAB, XLSX

(Submitter supplied) The recurrent mutation of histone variant H3.3 at glycine-34 (H3.3G34) defines a type of pediatric glioma. Characteristic changes to the epigenome associated with the disease are thought to be the consequence of altered methylation of the adjacent lysine-36 (K36) residue, but the complexity of this regulatory pathway in humans, combined with a multi-component disease etiology, has limited our understanding of how H3.3G34 mutations contribute to oncogenesis. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20660 GPL23150

12 Samples

Download data: BIGWIG, TDF