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:

GPL26551 GPL20705

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:

Other

Platform:

GPL20705

8 Samples

Download data: H5

(Submitter supplied) Cytosine methylation, a fundamental form of epigenetic regulation, is found in many eukaryotes and plays a significant role in cancer and other diseases. Using the genetically tractable model organism Neurospora crassa, we have identified genes that when mutated, cause the strains to be defective in methylation (dim). The process of DNA methylation in Neurospora has been shown to be dependent on DCDC, a five-member complex that directs the histone methyltransferase DIM-5 to tri-methylate Lysine 9 on histone H3 (H3K9me3). more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20705 GPL20660

3 Samples

Download data: TDF

(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

Platform:

GPL20705

32 Samples

Download data

(Submitter supplied) Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20705

12 Samples

Download data: FPKM_TRACKING, GTF

(Submitter supplied) Sensing and responding to light provides organisms an adaptive advantage, in part by altering gene expression. The complement of light-activated genes in model organisms is largely known, and some of the mechanisms by which proteins modulate the light response are likewise well defined. However, how light alters post translation modifications to chromatin and how changes in chromatin facilitates and/or inhibit changes in gene expression has not been examined in depth. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20705

20 Samples

Download data: BED

(Submitter supplied) ASH-1 orthologs are H3K36-specific methyltransferases that are conserved from fungi to humans but are poorly understood, in part because they are typically essential for viability. Here we examine the H3K36 methylation pathway of Neurospora crassa, which we find has just two H3K36 methyltransferases, ASH-1 and RNA polymerase II-associated SET-2. Our investigation of the interplay between SET-2 and ASH-1 uncovered a regulatory mechanism connecting ASH-1-catalyzed H3K36 methylation to repression of poorly transcribed genes. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL23150 GPL20705 GPL20660

18 Samples

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

(Submitter supplied) We performed high throughput sequencing of the transcriptome of N. crassa to quantify ultradian (<24h period) rhythms in the wild-type (FGSC#2489) and NCU02671 (msn-1) knockout (FGSC#11345) strains.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20705

24 Samples

Download data: CSV

(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) Development in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL20705 GPL20660

34 Samples

Download data: BEDPE, TDF, TSV, TXT

(Submitter supplied) Conidia germination is critical for fungi to colonize various habitats. We sampled RNA expression at four stages of conidia germination, including fresh conidia (15min), polar growth (120min), doubling of long axis (240min), and first hyphal branching (360min) in Neurospora crassa. Cultures were made on two different media, including Bird medium supporting only asexual development and maple sap medium supporting both asexual and sexual development, and two biological replicates were collected for all data points. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20705

24 Samples

Download data: TXT

(Submitter supplied) Purpose: The ∆col-26 mutant cannot utilize starch components and many other simple sugars efficiently. We employed RNA-seq based transcriptome profiling to reveal genes under the control of col-26. Method: We first obtained transcriptional data of Neurospora crassa WT on Vogel's minimal medium (VMM) without carbon source, on VMM with 2% sucrose, and on VMM with starch component, and transcriptional data of the ∆col-26 mutant on VMM with maltose or amylose. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20705 GPL16164

21 Samples

Download data: TXT

(Submitter supplied) Facultative heterochromatin in the filamentous fungus Neurospora crassa is identified by the repressive histone mark H3K27me3 and is primarily subtelomeric, while constitutive heterochromatin, marked by the DIM-5-catalzyed H3K9me3, is found at centromeres, telomeres, and smaller dispersed regions. In strains lacking constitutive heterochromatin (e.g., Δdim-5), H3K27me2/3 relocalizes to the regions formerly marked by H3K9me3. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL20705 GPL20660

16 Samples

Download data: BCF, FASTA, GTF, TDF, TXT, XLSX

(Submitter supplied) Eukaryotic genomes are organized into chromatin domains with distinct three-dimensional arrangements resulting from nucleic acid and protein factor interactions within the physical constraints of the nucleus. It is of obvious interest to determine interactions between various chromosomal regions defined by these nuclear constraints, and to identify important factors that limit the interactions. We used chromosome conformation capture (3C) followed by high-throughput sequencing (HiC) to improve our understanding of Neurospora crassa genome organization and to examine if known components of heterochromatin machinery influence nuclear organization. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL20705

5 Samples

Download data: FASTA, GTF, TDF, TXT

(Submitter supplied) Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL20705 GPL20660

22 Samples

Download data: TDF, TXT