GEO DataSets

(Submitter supplied) Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. more...

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24501

12 Samples

Download data: GTF, TAB

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

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24502 GPL24501

36 Samples

Download data

(Submitter supplied) Long noncoding RNA (lncRNA) plays important roles in morphological differentiation and development in eukaryotes. In filamentous fungi, however, little is known about lncRNAs and their roles in sexual development. Here we describe sexual stage-induced lncRNAs during the formation of perithecium, the sexual fruiting body of Fusarium graminearum. We identified 547 lncRNAs whose expression were developmental stage-specific; about 40% of them peaked during ascus development, when meiosis occurs. more...

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24501 GPL24502

24 Samples

Download data: GTF, TAB

(Submitter supplied) Fusarium graminearum and F. verticillioides are devastating cereal pathogens with very different life history and ecological characteristics. F. graminearum is homothallic, and sexual spores are an important component of its life cycle, responsible for disease initiation. F. verticilloides is heterothallic, and produces only modest numbers of fruiting bodies, which are not a significant source of inoculum. more...

Organism:

Fusarium verticillioides; Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19247 GPL19248

12 Samples

Download data: TXT

(Submitter supplied) Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) has been reported as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. This cosmopolitan species has also been reported as an opportunistic human pathogen, from infected soybean cyst nematodes, deer dung, and soil, and it possesses a highly active CO2 fixation mechanism. more...

Organism:

Fusarium graminearum; Fusarium neocosmosporiellum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24501 GPL25997

43 Samples

Download data: GFF, TAB

(Submitter supplied) Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3’ single-stranded (3’-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL13272

36 Samples

Download data: GFF, TXT

(Submitter supplied) Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: TXT

(Submitter supplied) Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. To dissect molecular mechanisms of small non-coding RNA-mediated gene regulation during ascospore production, we compared small RNA transcriptomes of fungal cultures harvested from F. graminearum wild-type strain Z-3639 and RNAi component mutants at 5 days after sexual induction.

Organism:

Fusarium graminearum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17573

7 Samples

Download data: TXT

(Submitter supplied) Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. To dissect molecular mechanisms of small non-coding RNA-mediated gene regulation during ascospore production, we compared transcriptomes of fungal cultures harvested from F. graminearum wild-type strain Z-3639 and RNAi component mutants at 5 days after sexual induction.

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17573

7 Samples

Download data: TXT

(Submitter supplied) Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. Conidiogenesis had been intensively studied in Aspergillus nidulans and regulatory pathway genes have been known to regulate conidiogenesis in stage specific manner. We reported the functional analyses of flbD, abaA, and wetA orthologs in F. graminearum. To understand genome-wide transcriptional profiling of conidiation, we employed RNA-seq of the wild-type Fusarium graminearum Z-3639 and each gene deletion mutants with three time courses (0 h, 6 h and 12 h after induction of conidiogenesis).

Organism:

Fusarium graminearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17573

14 Samples

Download data: TXT

(Submitter supplied) Chinese cordyceps is of particular interest for its confined distribution, mysterious lifecycle, ecological importance and developmental biology. The large scale artificial cultivation of this fungus has been succeeded in China until recently but with low efficiency and high cost being ascribed to too much unsolved biological issues, such as gene expression during development and the sexuality reproduction. more...

Organism:

Ophiocordyceps sinensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25863

18 Samples

Download data: XLS

(Submitter supplied) Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. more...

Organism:

Coprinopsis cinerea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16031

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of HeLa cells treated with α-amanitin for 9 h. Relative abundance to untreated control cells was used to evaluate the biogenesis of lncRNAs by RNA polymerase II.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) HeLa cells were fractioned in nucleus and cytoplasm to investigate the subcellular distribution of lncRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

2 Samples

Download data: TXT

(Submitter supplied) RNA aliquots were digested with 5’-phosphate-dependent exonuclease (5'-exo) following pre-treatment with tobacco acid pyrophosphatase (TAP) to release the 5’ cap and render the RNA susceptible to 5’ exonuclease digestion (TAP+/5'-exo+). Two color array hybridizations were performed and TAP+/5'-exo+ samples were compared with TAP-/5'-exo+ control samples.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of HeLa cells treated with actinomycin D for increasing amounts of time. Relative abundance to control cells was used to estimate the half-life of lncRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

20 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Mia PaCa 2 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of MCF-7 cells treated with 5-Aza for 96 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of DU-145 cells treated with 5-Aza for 72 h. Relative abundance to untreated control cells was used to estimate the effect of DNA demethylation on the expression of the RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL19372

4 Samples

Download data: TXT

(Submitter supplied) Using a 3'-tiling microarray covering the whole F. graminearum genes, we carried out genome-wide expression analyses of both a wild type and a FgVelB deletion strainn of F. graminearum at a sexual stage (3 days after perithecial induction on carrot agar) Our study is the first report elucidating regulatory pathways controlled by FgVelB in Fusarium graminearum.

Organism:

Fusarium graminearum

Type:

Expression profiling by array

Platform:

GPL15363

4 Samples

Download data: PAIR, PROBE