GEO DataSets

(Submitter supplied) In opportunistic human pathogenic fungi, changes in gene expression play a crucial role in the evolution of growth stages from early spore germination through host infection. Comparative transcriptomics from diverse fungal pathogens along closely related non-pathogenic model provided insights of regulatory mechanisms behind the initiation of infectious processes by different fungi. We examined the gene expression patterns of 3,845 single-copy orthologous genes (SCOGs) across five phylogenetically distinct species, including the opportunistic human pathogens Fusarium oxysporum, Aspergillus fumigatus, and A. more...

Organism:

Aspergillus nidulans; Fusarium oxysporum; Aspergillus fumigatus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL35000 GPL33056 GPL32392

45 Samples

Download data: TXT

(Submitter supplied) The transcription factor Mac1 is a key regulator of copper homeostasis and controls the transcriptional response to copper-limiting conditions in fungi. Expression analyses performed in the soil-borne plant pathogen Fusarium oxysporum revealed that almost all copper starvation-induced genes are downregulated in the absence of the regulator Mac1. The aim of this ChIP-seq analysis is to elucidate which of these genes are direct targets of Mac1.

Organism:

Fusarium oxysporum f. sp. lycopersici 4287

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33791

9 Samples

Download data: WIG

(Submitter supplied) The transcription factor Mac1 is a key regulator of copper homeostasis, controlling the transcriptional response to copper-limiting conditions in fungi. It has been described as a virulence factor in human pathogens such as Candida albicans and Aspergillus fumigatus, but surprisingly its role in plant pathogenesis is poorly understood. Targeted deletion of Mac1 in the soilborne pathogen Fusarium oxisporum results in an inability to grow under copper-limited conditions and kills tomato plants. more...

Organism:

Fusarium oxysporum f. sp. lycopersici 4287

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33765

24 Samples

Download data: SF

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

Organism:

Fusarium fujikuroi; Fusarium oxysporum f. sp. lycopersici

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) In plant pathogenic fungi, conditionally dispensable (CD) chromosomes are often associated with virulence, but not viability. Such virulence-associated CD chromosomes carry genes encoding effectors and/or host-specific toxin biosynthesis enzymes, potentially important for determining host specificity. Fusarium oxysporum causes devastating diseases of more than 100 plant species. In particular, F. oxysporum f. more...

Organism:

Arabidopsis thaliana; Fusarium oxysporum; Brassica oleracea

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19580 GPL29143 GPL29144

25 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Fusarium oxysporum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17639 GPL26208 GPL24159

58 Samples

Download data: TXT

(Submitter supplied) Background: Cell walls (CWs) are protein-rich polysaccharide matrices essential for plant growth and environmental acclimationadaptation. The CW constitutes the first physical barrier as well as a primary source of sugars for plant microbes, such as the  vascular pathogen Fusarium oxysporum (Fo). Fo colonizes roots, advancing through the plant primary CWs towards the vasculature, where it grows causing devastation in many crops. more...

Organism:

Fusarium oxysporum; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24159 GPL17639

52 Samples

Download data: TXT, XLSX

(Submitter supplied) Using next-generation sequencing, we sequenced transcriptomes of A. thaliana plants infected by the pathogenic and the symbiotic fungus and analyzed plant and fungal gene expression changes between pathogenic and symbiotic interactions. Infected plants were sampled at early infection stages, 12, 24, 48 and 96 HPI (hours post inoculation)

Organism:

Fusarium oxysporum; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL22481

29 Samples

Download data: TXT

(Submitter supplied) To further understand the abnormal phenotype of the calcineurin mutant strains and identify calcineurin-mediated genes in F. oxysporum f. sp. lycopersici, we performed RNA sequencing to compare the transcriptome profiles of the wild-type (WT), Δcna1(HFW1) and Δcnb1 (HFW3) mutants. By pairwise analysis, a total of 2139 genes were differentially expressed between WT and Δcna1 mutant based on the selection criteria of four-fold change in expression (Log2 fold change > 2 or < -2, P < 0.05). more...

Organism:

Fusarium oxysporum f. sp. lycopersici 4287

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27462

3 Samples

Download data: TXT

(Submitter supplied) Background: The fungal pathogen, Fusarium oxysporum f.sp. pisi (Fop) causes fusarium wilt in peas. Races 1, 2, 5 and 6 are responsible for the majority of the economic losses globally. These are the only races present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales however, there has been no Fop-pea pathosystem studies. Results: A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. more...

Organism:

Fusarium oxysporum f. sp. pisi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29262

48 Samples

Download data: TXT

(Submitter supplied) nox1 gene has effect on the production of H2O2 of T. guizhouense NJAU4742. In this experiment, WT, knockout mutant and overexpression mutant of nox1 gene for NJAU4742 were used to do confrantation with F. oxysporum FOC4 strain, and then the mycelum from NJAU4742 and FOC4 (before contact and after contact) were collected and used to detect the gene expression patterns in this progress by RNA-seq.

Organism:

Trichoderma guizhouense; Fusarium oxysporum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25399 GPL25398 GPL22481

27 Samples

Download data: XLSX

(Submitter supplied) To study whether there are differences in chromatin-mediated regulation between and within chromosomes in Fusarium oxysporum f. sp. lycopersici 4287 (FGSC9935), we determined the distribution of histone marks associated with euchromatin (H3K4me2) and facultative heterochromatin (H3K27me3) in vitro. We then determined whether these differences correlate with differences in dispensability and sequence divergence and gene expression.

Organism:

Fusarium oxysporum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24159

4 Samples

Download data: BED

(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) Temperature shift experiment to assay heat stress response

Organism:

Fusarium oxysporum f. sp. lycopersici 4287

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24908

6 Samples

Download data: TXT

(Submitter supplied) Thymol (5-methyl-2-(1-methylethyl) phenol, PubChem CID: 6989) has been extensively reported to have antimicrobial activity against pathogenic microorganisms. In this study, the growth of F. oxysporum was significantly inhibited by thymol in vitro. The dry weight of F. oxysporum was decreased significantly. Thymol-induced cell membrane damage was observed at 24 hpi (hours post incubation). Therefore, the changes in the gene expression level of F. more...

Organism:

Fusarium oxysporum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24159

6 Samples

Download data: TXT

(Submitter supplied) We provide genome sequences of altogether 9 F. fujikuroi and one F. oxysporum (outgroup) strains, all isolated from rice plants in different geographical regions of the world, and searched for differences in genome structure, chromosome size, secondary metabolite production, virulence on rice, and in vitro and in planta transcriptome profiles. Despite their high relatedness on genome level, they differ significantly in their ability to infect rice, to form asexual spores (micro-and macroconidia), and to produce secondary metabolites. more...

Organism:

Fusarium oxysporum; Fusarium fujikuroi

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22481 GPL22633

30 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 spp. are fungal pathogens of humans and plants. Fusarium oxysporum and Fusarium solani are important species isolated from infections such as onychomycosis, fungal keratitis, invasive infections, and disseminated diseases. These pathologies have a very difficult therapeutic management and poor therapeutic responses, especially in patients with disseminated infection. Little information is available regarding the molecular mechanisms responsible for antifungal resistance in these fungi. more...

Organism:

Fusarium oxysporum; Fusarium solani

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21965 GPL21966

6 Samples

Download data: TSV

(Submitter supplied) Deep sequencing of mRNA from Fusarium oxysporum f. sp. Cubense 1 and 4 after infecting Musa acuminata 0h and 48h.

Organism:

Fusarium oxysporum f. sp. cubense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16015

4 Samples

Download data: WIG