GEO DataSets

(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) 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:

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:

Methylation profiling by high throughput sequencing

Platforms:

GPL23150 GPL16164

5 Samples

Download data: BIGWIG, IGV

(Submitter supplied) In this work, we reported that STK-12 functions as a novel repressor of cellulase expression. The stk-12 disruption strain not only displayed enhanced cellulase production but also retained a steady state, with high expression levels of cellulase genes, for longer than the wild type strain.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

16 Samples

Download data: XLSX

(Submitter supplied) By analyzing genome-wide transcriptional responses to deletion of each of two MAP kinase coding genes mak-2 (PR-MAP kinase pathway) and mak-1 (CWI-MAP kinase pathway) in Neurospora crassa during protoperithecium formation, 430 genes co-regulated by MAK-1 and MAK-2 were found, functionally enriched at integral components of membrane and oxidoreductase.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

6 Samples

Download data: XLS

(Submitter supplied) In yeast and mammals, activated GCN2 can phosphorylate its substrate eIF2α, which is a part of the eIF2-GTP-Met-tRNAiMet ternary complex. The eIF2α phosphorylation blocks the ternary complex formation and therefore inhibits translation initiation. Meanwhile, GCN2 activation associates with ribosomes and some translation elongation factors such as eEF1A. In Neurospora crassa, the homolog of GCN2 is CPC-3. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29831 GPL16164

33 Samples

Download data: TXT

(Submitter supplied) Fungal degradation of lignocellulosic biomass requires various (hemi-)cellulases and plays key roles in biological carbon cycle. Although cellulases induction recently described in some saprobic filamentous fungi, regulation of cellulase transcription has not been studied thoroughly. Here, we identified and characterized the novel cellulase regulation factors clr-4 in Neurospora crassa and its ortholog Mtclr-4 in Myceliophthora thermophila. more...

Organism:

Neurospora crassa; Thermothelomyces thermophilus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24572 GPL16164

6 Samples

Download data: XLSX

(Submitter supplied) Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of proline, branched chain amino acids, and aromatic amino acids. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16164 GPL23150

86 Samples

Download data: TXT, XLSX

(Submitter supplied) Both H3K9me3 and DNA methylation are subject to spreading mechanisms to effectively cover incipient chromatin across heterochromatin domains. Boundary elements and associated limiting factors are necessary to prevent heterochromatin from spreading into neighboring, gene-rich heterochromatin. LSD1 was identified to be one such factor, given previous studies in other models and high conservation throughout eukaryotes. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL23150 GPL16164 GPL20660

16 Samples

Download data: BED, BIGWIG, IGV, TDF, TXT

(Submitter supplied) The high throughput mRNA-seq technology was used to measure the effect of cpc-1 deletion on transcriptome change of Neurospora crassa grown under different culture conditions using standard Illumina protocols.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26551 GPL16164

18 Samples

Download data: TXT

(Submitter supplied) The silencing of tRNA-specific adenosine deaminase adat2 in Neurospora crassa abolished most of the I34 modification, resulting in major tRNA profile changes. The adat2 silencing caused genome-wide codon usage-biased ribosome pausing on mRNAs corresponding to changes in the tRNA profile, which reprograms translation elongation kinetics on ADAT-related codons. The ribosome profiling in this study was used to measure the effect of defective I34 modification of the eight tRNAs on translation kinetics during elongation stage. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16164 GPL26551

12 Samples

Download data: TXT

(Submitter supplied) Purpose: We utilized high-throughput genomic approach to investigate transcriptional changes in two Neurospora crassa strains, the Δpac-3 knockout strain, and the Δmus-52 strain, under limited and sufficient Pi availability conditions, to evaluate the effects of the Δpac-3 deletion in gene modulation, from a plant-pathogen perspective. Methods: All strains were maintained on solid Vogel’s Minimal (VM) medium supplemented with 2 % sucrose at 30 °C and pH 5.8. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: CSV, TXT

(Submitter supplied) Analysis of differentially spliced sites at DD12 and DD20

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

2 Samples

Download data: TXT

(Submitter supplied) Aberrant DNA methylation is often associated with cancers and DNA-demethylating agents such as 5-azacytidine (5-azaC) are often used for anti-tumor therapy. Although it is clinically effective at inhibiting DNA methylation, the mechanistic effect that 5-azaC elicits on eukaryotic cells is controversial. It has been proposed that incorporation of 5-azaC into DNA during replication irreversibly tethers cytosine methyltransferases (MTases) to DNA. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16164 GPL20660

19 Samples

Download data: FASTA, IGV, TDF, TXT, VCF, WIG

(Submitter supplied) Purpose: We utilised high-throughput genomic approache to investigate transcriptional changes in two Neurospora strains (74A [wild-type] and mutant Δmus-52), under different phosphate availability conditions to evaluate the effects of mus-52 deletion in gene transcriptional modulation, and thus, infer its influence regarding metabolic response to changing extracellular levels of inorganic phosphate (Pi). more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: CSV, TXT

(Submitter supplied) In this study, we screened morphological mutants in the filamentous fungus N. crassa. Of the 90 morphological mutants screened, 14 mutants exhibited considerably higher viscosity compared with that of the wild type strain, and only 2 mutants showed low-viscosity morphologies in submerged culture. We observed that disruption of gul-1 (NCU01197), which encodes an mRNA binding protein involved in cell wall remodeling, caused pellet formation as the fermentation progressed, and resulted in the most significant decrease in viscosity of culture broth. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

2 Samples

Download data: XLSX

(Submitter supplied) We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies. The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression. In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL16164 GPL17918 GPL20705

8 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Identifying nutrients available in the environment and utilizing them in the most efficient manner is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of carbohydrates, from simple sugars to the complex carbohydrates found in plant cell walls. The zinc binuclear cluster transcription factor CLR-1 is necessary for utilization of cellulose, a major, recalcitrant component of the plant cell wall; however, expression of clr-1 in the absence of an inducer is not sufficient to induce cellulase gene expression. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23150 GPL16164

42 Samples

Download data: TXT

(Submitter supplied) The ability to rationally engineer filamentous fungi could greatly facilitate biotechnological enzyme production for the degradation of plant cell wall polysaccharides in biorefinery applications. However, an incomplete and fragmented knowledge base of the biomolecular networks responsible for plant cell wall deconstruction by filamentous fungi impedes experimental efforts in this direction. To expand this knowledge base, we have reconstructed a detailed network of those reactions occurring in the filamentous fungus Neurospora crassa that are important for the degradation of plant cell wall polysaccharides into simple sugars. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

12 Samples

Download data: FPKM_TRACKING