GEO DataSets

(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) 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) 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) 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) 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:

GPL16164 GPL26551

18 Samples

Download data: TXT

(Submitter supplied) Cryptochromes were identified in plants and animals where they function as either photoreceptors or circadian clock components. In the filamentous fungus Neurospora, the biological function of cryptochrome has not yet been explored. Here, we demonstrate that Neurospora crassa cryptochrome (Nc cry) is a DASH-type of cryptochrome, capable of binding FAD and MTHF, whose transcript and protein levels are both strongly induced by blue light in a wc-1 dependent manner. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL8206

12 Samples

Download data: TXT

(Submitter supplied) To better understand the roles of WC-1, WC-2 and other putative photoreceptors in mediation of light signals and to identify new components in light sensing cascades, we used microarrays with genome-wide coverage to characterize light-inducible transcriptional changes in Neurospora crassa. After unsupervised hierarchical clustering of 90 microarrays, 316 genes, representing about 3.21% of the total genome, showed robust and consistent light responses. more...

Organism:

Neurospora crassa

Type:

Expression profiling by array

Platform:

GPL5796

135 Samples

Download data: DAT

(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) 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) 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) The molecular circadian clock, which controls rhythmic 24-hour oscillation of genes, proteins, and metabolites, is disrupted across many human cancers. Deregulated expression of MYC oncoprotein has been shown to alter expression of molecular clock genes, leading to a disruption of molecular clock oscillation across cancer types. It remains unclear what benefit cancer cells gain from suppressing clock oscillation, and how this loss of molecular clock oscillation impacts global gene expression and metabolism in cancer. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

26 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

185 Samples

Download data

(Submitter supplied) The molecular circadian clock, which controls rhythmic 24-hour oscillation of genes, proteins, and metabolites, is disrupted across many human cancers. Deregulated expression of MYC oncoprotein has been shown to alter expression of molecular clock genes, leading to a disruption of molecular clock oscillation across cancer types. However, it remained unclear how this loss of molecular clock oscillation impacted global gene expression and metabolism in cancer, and what benefit cancer cells might gain from suppressing clock oscillation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

76 Samples

Download data: TXT

(Submitter supplied) The molecular circadian clock, which controls rhythmic 24-hour oscillation of genes, proteins, and metabolites, is disrupted across many human cancers. Deregulated expression of MYC oncoprotein has been shown to alter expression of molecular clock genes, leading to a disruption of molecular clock oscillation across cancer types. However, it remained unclear how this loss of molecular clock oscillation impacted global gene expression and metabolism in cancer, and what benefit cancer cells might gain from suppressing clock oscillation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

83 Samples

Download data: TXT

(Submitter supplied) To investigate the role of epigenetic modifications H3K27me3 and h3r17me2 in aging.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

24 Samples

Download data: BIGWIG, BROADPEAK

(Submitter supplied) METTL16 is a well-characterized m6A methyltransferase that has been reported to contribute to tumorigenesis in various types of cancer. However, the effect of METTL16 on tumor progression under restricted nutrient conditions, which commonly occur in tumor microenvironment, has yet to be elucidated. Herein, our study initially reported the inhibitory effect of METTL16 depletion on apoptosis under amino acid starvation conditions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) METTL16 is a well-characterized m6A methyltransferase that has been reported to contribute to tumorigenesis in various types of cancer. However, the effect of METTL16 on tumor progression under restricted nutrient conditions, which commonly occur in tumor microenvironment, has yet to be elucidated. Herein, our study initially reported the inhibitory effect of METTL16 depletion on apoptosis under amino acid starvation conditions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: TXT