GEO DataSets

(Submitter supplied) The observation that light led to a large reduction in the number of perithecia in the ∆ve-1 strain suggested that WC-1, the photoreceptor component of the WCC transcription factor complex, may participate in this regulation. Therefore, we analyzed the sexual phenotype of a double mutant with deletions in ve-1 and wc-1

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

24 Samples

Download data: TXT

(Submitter supplied) Repression of facultative heterochromatin is essential for developmental processes in numerous organisms. Methylation of histone H3 lysine 27 (H3K27) by Polycomb repressive complex 2 is a prominent feature of facultative heterochromatin in both fungi and higher eukaryotes. Although this methylation is frequently crucial for silencing, the detailed mechanism of repression remains poorly understood. more...

Organism:

Neurospora crassa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26551 GPL20660 GPL23150

32 Samples

Download data: BW

(Submitter supplied) Repression of facultative heterochromatin is essential for developmental processes in numerous organisms. Methylation of histone H3 lysine 27 (H3K27) by Polycomb repressive complex 2 is a prominent feature of facultative heterochromatin in both fungi and higher eukaryotes. Although this methylation is frequently crucial for silencing, the detailed mechanism of repression remains poorly understood. more...

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23150 GPL26551

14 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; 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:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26551

3 Samples

Download data: BEDGRAPH, BIGWIG

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

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

24 Samples

Download data

(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 onPDA, iand two biological replicates were collected for all data points. The growth was under a labratory condition of 25C and constant light.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

12 Samples

Download data: CSV, 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 Bird medium, and two biological replicates were collected for all data points. The growth was under a labratory condition of 375C and constant light.

Organism:

Neurospora crassa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26551

12 Samples

Download data: CSV, TXT

(Submitter supplied) Establishing and maintaining appropriate gene repression is critical for the health and development of multicellular organisms. Histone H3 lysine 27 (H3K27) methylation is a chromatin modification associated with repressed facultative heterochromatin, but the mechanism of repression remains unclear. We used a forward genetic approach to identify novel genes involved in transcriptional silencing of H3K27 methylated chromatin in the filamentous fungus, Neurospora crassa. 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

Platforms:

GPL26551 GPL23150

59 Samples

Download data: BW, TXT

(Submitter supplied) For a eukaryotic genome to properly function, its chromatin must be precisely organized, as genome topology impacts transcriptional regulation, cell division, DNA replication, and DNA repair, among other essential processes. Disruption of human genome topology can lead to disease states, such as cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) technologies to assess genome organization has revolutionized our understanding of the arrangement of chromosomes within the nuclear genome. more...

Organism:

Neurospora crassa

Type:

Other

Platforms:

GPL26551 GPL23150

10 Samples

Download data: FASTA, GTF, H5

(Submitter supplied) Crucial mechanisms are required to restrict self-propagating heterochromatin spreading within defined boundaries and prevent euchromatic gene silencing. In the filamentous fungus Neurospora crassa, the JmjC domain protein DNA METHYLATION MODULATOR-1 (DMM-1) prevents aberrant spreading of heterochromatin, but the molecular details remain unknown. Here, we revealed that DMM-1 is highly enriched in a well-defined 5-kb heterochromatin domain and constrained its aberrant spreading. more...

Organism:

Neurospora crassa

Type:

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

Platforms:

GPL26551 GPL31176

36 Samples

Download data: BEDGRAPH, BW

(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) 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) 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