GEO DataSets

(Submitter supplied) The MAK-1 pathway is the least characterized MAP kinase pathway in Neurospora. Microarray analyses were carried out to identify genes with altered expression in Δmak-1 as compared to wild type strains. Mycelial mats of wild type and Δmak-1 strains were grown in constant light (LL) at 25C for 2 and 6 days, respectively, in 1X Vogel’s, 2% glucose, 0.5% Arginine HCl, pH 6.0. A cork borer was used to cut plugs to inoculate 75mL of the same liquid media and cultures were grown in LL at 25C for 24h, transferred to constant darkness (DD) 25C for 24 h before being harvested and total RNA extracted.

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL10640

5 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Neurospora crassa ∆mak-2 strain grown under phosphate-shortage were compared the transcription profile of the control strain grown in both low- and high-Pi cultures. The filamentous fungus Neurospora crassa provides an excellent model system for the study of molecular responses to ambient signaling in eukaryotic microorganisms. Inorganic phosphate is an essential growth-limiting nutrient in nature and is crucial in genetic information. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL14949

16 Samples

Download data: TXT

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

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30082 GPL20660

160 Samples

Download data: TXT

(Submitter supplied) We report the genome-wide impact of rhythmic P-eIF2α levels in vivo by performing ribosome profiling and RNA-seq in Neurospora crassa samples grown over a circadian time course. We identified candidate genes which showed rhyhmic ribosome occupancy in WT cells but lost rhythms in mRNA levels and ribosome occupancy in the clock mutant Dfrq, eIF2α kinase knockout Dcpc-3, and constitutively active kinase mutant cpc-3c cells. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL20660 GPL30082

80 Samples

Download data: TXT

(Submitter supplied) We report the genome-wide impact of rhythmic P-eIF2α levels in vivo by performing ribosome profiling and RNA-seq in Neurospora crassa samples grown over a circadian time course. We identified candidate genes which showed rhyhmic ribosome occupancy in WT cells but lost rhythms in mRNA levels and ribosome occupancy in the clock mutant Dfrq, eIF2α kinase knockout Dcpc-3, and constitutively active kinase mutant cpc-3c cells. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30082 GPL20660

80 Samples

Download data: TXT

(Submitter supplied) The aim of this analysis was the identification of candidate genes that might be regulated in a circadian manner in the filamentous ascomycete Pyronema confluens. The fungus was grown in submerged culture to promote vegetative growth, and after a period in constant light, the samples were shifted to darkness (DD). Cultures were sampled after 24 and 36 hours in DD. The samples were used for RNA-seq analysis, and candidate genes with significantly higher expression after 24 vs. more...

Organism:

Pyronema omphalodes CBS 100304

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19175

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq from Neurospora crassa at 5 time points of light induction, with 2 replicates for each, totalling 10 samples

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

10 Samples

Download data: TXT

(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) Analysis of genes differentially expressed in wild type and upf1 knockout strains

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16164

2 Samples

Download data: TXT

(Submitter supplied) The period-2 (prd-2) mutant of Neurospora crassa is characterized by recessive inheritance of a 26-hour long period phenotype of the circadian clock. PRD-2 encodes a putative RNA-binding protein. To identify PRD-2 target genes and its role in the clock, we performed transcript profiling in delta prd-2 compared to control samples using RNA-Sequencing. Hundreds of genes are affected by loss of prd-2, including decreased levels of Casein Kinase I (ck-1a, NCU00685). more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

6 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) To study the consequences of transcription factor pp-1 deletion during vegetative cell fusion, we sequenced mRNA of WT and Δpp-1 conidia during a period of intense germling fusion activity .

Organism:

Neurospora crassa OR74A

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17654

2 Samples

Download data: TXT

(Submitter supplied) To study the consequences of transcription factor pp-1 deletion during vegetative cell fusion, we performed whole genome microarrays of WT and Δpp-1 conidia during their initial growth period (3h - 8h).

Organism:

Neurospora crassa; Neurospora crassa OR74A

Type:

Expression profiling by array

Platform:

GPL13956

35 Samples

Download data: GPR, TXT

(Submitter supplied) To study the consequences of MAK-2 activity modulation during vegetative cell fusion, we took advantage of a previously constructed allele of MAK-2 (MAK-2Q100G) to specifically perturb kinase signaling during germling vegetative cell fusion (inhibition of MAK-2Q100G activity by addition of the ATP analog 1NM-PP1 results in a phenotype indistinguishable from mak-2 deletion strains). Whole genome microarrays of mak-2Q100G cells following 20 min 1NM-PP1 treatment were performed.

Organism:

Neurospora crassa OR74A; Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL13956

7 Samples

Download data: GPR

(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) The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide mRNA binding protein (RBP) that can associate with 828 “core” mRNA species. When cell wall integrity (CWI) is challenged, the repertoire of associated RNA species increases up to 2628 mRNAs (including its own transcript). GUL-1 can bind mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmatic reticulum (ER), as well as CWI and osmoregulatory response MAPK pathway components. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

22 Samples

Download data: CSV

(Submitter supplied) Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30082

12 Samples

Download data: TXT, XLSX

(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) 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) 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