GEO DataSets

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

Organism:

Fusarium oxysporum f. sp. lycopersici; Fusarium fujikuroi

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24816 GPL22633 GPL34083

14 Samples

Download data

(Submitter supplied) RNA interference (RNAi) mechanisms play key regulatory roles in many biological systems, and components of the RNAi pathway are conserved in a wide range of eukaryotic genomes, including those of filamentous fungi. The biotechnological fungus Fusarium fujikuroi, widely used in secondary metabolism studies, contains the complete set of genes expected for RNAi pathways, including dcl1 and dcl2 dicer genes. more...

Organism:

Fusarium fujikuroi; Fusarium oxysporum f. sp. lycopersici

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL34083 GPL22633

8 Samples

Download data: CSV

(Submitter supplied) we found a new population of 31nt sRNAs that results from the addition of a non-templated 3-4 adenosine nucleotides at the 3´-end of the 27nt sRNA populations. We sequenced various sRNA libraries including both total RNAs and IP-ed RNAs of EhAgo proteins.

Organism:

Entamoeba invadens; Entamoeba histolytica

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL19934 GPL19933

13 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) Digital gene expression profiling analysis of the mycelium growth and conidiogenesis stages of Metarhizium robertsii

Organism:

Metarhizium robertsii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16039

4 Samples

Download data: XLSX

(Submitter supplied) The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. more...

Organism:

Oryza sativa; Pyricularia oryzae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9316 GPL16451

8 Samples

Download data: TXT

(Submitter supplied) To explore the presence of milRNA in Fusarium oxysporum f. sp. niveum (Fon) and evaluate their expression at different propagules, two categories of sRNAs were identified from Fon hyphae and microconidia by using illumina sequencing. A total of 650,960 and 561,114 unique sRNAs were obtained from the hyphae and microconidia samples. With a previously constructed pipeline to search for microRNA, we then identified 74 and 56 miRNA-like small RNAs (milRNAs) candidates in hyphae and microconidia based on the short hairpin structure analysis, respectively. more...

Organism:

Fusarium oxysporum f. sp. niveum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22156

2 Samples

Download data: FA, TXT

(Submitter supplied) Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was described about 100 years ago as the causative agent of Bakanae (“foolish seedling”) disease of rice. Apart from GAs, the fungus is known to produce pigments and mycotoxins, but the biosynthetic genes are known for only eight products. more...

Organism:

Fusarium fujikuroi

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17016

4 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289 under gibberellin-inducing and -repressing conditions. Fusarium fujikuroi is a biotechnologically important fungus due to its almost unique ability to produce gibberellic acids (GAs), a family of phytohormones. The fungus was already described about 100 years ago as the causative agent of Bakanae (foolish seedling) disease of rice. more...

Organism:

Fusarium fujikuroi

Type:

Expression profiling by array

Platform:

GPL16547

15 Samples

Download data: PAIR

(Submitter supplied) In the fungi Fusarium fujikuroi and Fusarium oxysporum, the induction of carotenogenesis by light and its deregulation in carS mutants, affected in a protein of the RING-finger family, are achieved on transcription of the structural genes of the pathway, some of them organized in a cluster. We have carried out global RNAseq transcriptomics analyses to investigate the relationship between the regulatory effects of light and the carS mutation. more...

Organism:

Fusarium fujikuroi; Fusarium oxysporum f. sp. lycopersici

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24303 GPL24306

20 Samples

Download data: TSV

(Submitter supplied) The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to identify small RNA-derived transcript cleavage sites from both barley and Bgh that regulate gene expression at the post-transcriptional level both within species and cross-kingdom.

Organism:

Hordeum vulgare; Blumeria hordei

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23699

5 Samples

Download data: CSV, PDF

(Submitter supplied) Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to identify small RNAs (sRNAs) from both barley and Bgh that regulate gene expression both within species and cross-kingdom.

Organism:

Hordeum vulgare; Blumeria hordei

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23699

90 Samples

Download data: CSV, PDF

(Submitter supplied) Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012). B. graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to address the temporal regulation of membrane trafficking associated gene expression in barley-powdery mildew interactions. more...

Organism:

Hordeum vulgare; Blumeria hordei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23699

90 Samples

Download data: CSV, PDF

(Submitter supplied) The proteins of the White Collar 1 family (WC) constitute a major class of flavin photoreceptors, widely distributed in fungi, that work in cooperation with a WC 2 protein forming a regulatory complex. The WC complex was investigated in great detail in Neurospora crassa, a model fungus in photobiology studies, where it controls all its major photoresponses. The fungus Fusarium fujikuroi, a model system in the production of secondary metabolites, contains a single WC-1 gene called wcoA. more...

Organism:

Fusarium fujikuroi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24816

24 Samples

Download data: TSV

(Submitter supplied) To explore the effect of stable RNAi on the small RNA (sRNA) population in wheat, we constructed a sRNA library from hexaploid wheat that expresses an RNAi construct under the 35S promoter that targets the endogenous NO APICAL MERISTEM (TaNAM) gene. The presence of this RNAi transgene causes a 40% reduction in expression of the target genes as measured by quantitative RT-PCR and significantly delays senescence and reduces remobilization of N, Fe, and Zn to the grain.

Organism:

Triticum aestivum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10467

1 Sample

Download data: TXT

(Submitter supplied) Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and a leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. more...

Organism:

Streptococcus pneumoniae D39

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25906

10 Samples

Download data: TXT

(Submitter supplied) Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and the leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. more...

Organism:

Streptococcus pneumoniae D39

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25906

6 Samples

Download data: BW

(Submitter supplied) This experiment describes small RNA gene expression after treatment of Arabidopsis seedlings with elicitors obtained from the fungus F. oxysporum

Organism:

Arabidopsis thaliana; Caenorhabditis elegans; Drosophila melanogaster

Type:

Non-coding RNA profiling by array

Platform:

GPL19024

12 Samples

Download data: GPR

(Submitter supplied) In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19476

4 Samples

Download data: XLS