GEO DataSets

(Submitter supplied) Proper mitochondrial function is critical for the ability of the fungal pathogen Cryptococcus neoformans to cause disease. Mitochondrial dysfunction of WT cells treated with antimycin A or L-DOPA, or on cells lacking Cir1 is evident from this dataset. These experiments revealed influences on transcript levels of genes encoding Fe-S cluster assembly components and the response to oxidative stress in Cryptococcus neoformans.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24579

15 Samples

Download data: TXT

(Submitter supplied) Cryptococcus neoformans (Cn) is an opportunistic fungal microorganism that causes life-threatening meningoencephalitis. During the infection, the microbial population is heterogeneously composed of cells with varying generational ages, with older cells accumulating during chronic infections. This is attributed to their enhanced resistance to phagocytic killing and tolerance of antifungals like fluconazole (FLC). more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28713

4 Samples

Download data: TXT

(Submitter supplied) We isolated a bacterial identified as the genus of Mycetocola from the infected Flammulina velutipes samples collected from mushroom house in Hebei, North China. The stipe of F. velutipes appeared water-soaked, soften and browning after infected, finally, the whole plant rotten. The incidence of the disease can reach more than 80% in the serious areas, resulting in an obvious decline in the yield and quality of the F. more...

Organism:

Flammulina velutipes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24716

9 Samples

Download data: TXT

(Submitter supplied) The human gut is inhabited by a complex ecosystem of microorganisms, encompassing bacteria, viruses, protozoa, and fungi. Recent research has illuminated the significance of the gut fungal microbiota (mycobiota) in shaping host immunity and influencing the onset and progression of various human diseases. While most investigations into gut microbiota have centered on bacteria, accumulating evidence has underscored the role of mycobiota in the development of inflammatory bowel diseases (IBD), including both ulcerative colitis (UC) and Crohn's disease (CD). more...

Organism:

Malassezia globosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34157

16 Samples

Download data: TSV

(Submitter supplied) During mammalian colonization and infection, microorganisms must be able to rapidly sense and adapt to changing environmental conditions including alterations in extracellular pH. The fungus-specific Rim/Pal signaling pathway is one process that supports microbial adaptation to alkaline pH. This cascading series of interacting proteins terminates in the proteolytic activation of the highly conserved Rim101/PacC protein, a transcription factor that mediates microbial responses that favor survival in neutral/alkaline pH growth conditions, including many mammalian tissues. more...

Organism:

Malassezia sympodialis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34153

27 Samples

Download data: TXT

(Submitter supplied) The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded programme. Fruiting bodies reached highest complexity levels in the Agaricomycetes, yet, the underlying genetics is currently poorly known. In this work, we functionally characterised an unannotated gene we term snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologues of snb1 are present in almost all Agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. Snb1 mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed a multitude of differentially regulated genes and gene families that may be related to tissue differentiation and the formation of structures. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying tissue differentiation in the Agaricomycetes.

Organism:

Coprinopsis cinerea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33837

12 Samples

Download data: CSV, FASTA, GTF

(Submitter supplied) To investigate the role of lncRNAs in postharvest senescence of Sparassis latifolia, We stored the fruiting bodies of S. latifolia at 4 ℃ for 0, 8, 16 and 24 days with OPP film packaging after harvest and profiled the lncRNA and mRNA transcriptome. We then performed gene expression profiling analysis using data obtained from RNA-seq of fruiting body at 4 time points.

Organism:

Sparassis latifolia

Type:

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

Platform:

GPL33214

12 Samples

Download data: TXT

(Submitter supplied) Bacterial persisters, a subpopulation of genetically susceptible cells that are normally dormant and tolerant to bactericides, have been studied extensively because of their clinical importance. In comparison, much less is known about the determinants underlying fungicide-tolerant fungal persister formation in vivo. Here, we report that during mouse lung infection, Cryptococcus neoformans forms persisters that are highly tolerant to amphotericin B (AmB), the standard of care for treating cryptococcosis. more...

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33437

27 Samples

Download data: XLSX

(Submitter supplied) Fungal infections have become a clinical challenge due to the emergence of drug-resistance of invasive fungi and a rapid increase of novel pathogens. The development of drug resistance has further restricted the use of antifungal agents. Therefore, there is anurgentneedto searchforalternativetreatmentoptions for Cryptococcus neoformans (C. neoformans). Disulfiram (DSF) has a high human safety profile and promising applications as an antiviral, antifungal, antiparasitic, and anticancer agent. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28713

6 Samples

Download data: TXT

(Submitter supplied) To investigate the pleiotropic roles of Lkh1 in stress response and virulence, we constructed lkh1∆ mutant strains. In this study, we found that Tor1 was an upstream regulator of Lkh1 in C. neoformans. We then performed gene expression profiling analysis to elucidate signaling circuitry downstream of CnLkh1 in the TOR1-Lkh1 pathway using data obtained from RNA seq of 2 different strains (WT of lkh1∆ mutant) with or without rapamycin treatment.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33437

12 Samples

Download data: TXT

(Submitter supplied) Casein kinase 2 (CK2) is a potential therapeutic target for several human diseases due to its crucial roles in growth, differentiation, and metabolic homeostasis. This study delves into the role of the CK2 complex in Cryptococcus neoformans, a key fungal pathogen causing meningitis. In C. neoformans, the CK2 complex is made up of a main catalytic subunit (Cka1) and two regulatory subunits (Ckb1 and Ckb2). more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21073

9 Samples

Download data: CSV

(Submitter supplied) Gene expression of FB2 wt in minimal medium with 2 percent arabinose or glucose after 24h of growth was compared with the conditional promoter regulated strain Pcrg1:grx4 (#55). Glucose is a repressor of this promoter while arabinose acts as inducer. Grx4 was initially pre-depleted during growth on MM with glucose over night. Afterwards cells were transferred to MM with either glucose or arabinose and cells were collected after 24h. more...

Organism:

Ustilago maydis 521

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31263

12 Samples

Download data: CSV

(Submitter supplied) In bacteria, antibiotic tolerance, the ability of a susceptible population to survive high doses of cidal drugs, has been shown to compromise therapeutic outcomes. In comparison, whether fungicide tolerance can be induced by host-derived factors during fungal diseases remains unproven. Here, through a systematic evaluation of metabolite-drug-fungal interactions in the leading fungal meningitis pathogen, Cryptococcus neoformans, we found that glucose, on which the brain depends for fuel, induces fungal tolerance to amphotericin B (AmB) in mouse brain tissue and patient cerebrospinal fluid via the fungal glucose repression activator Mig1. more...

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24579

72 Samples

Download data: XLSX

(Submitter supplied) Ectomycorrhizal (ECM) fungi are crucial for tree nitrogen (N) nutrition, however, mechanisms governing N transfer from fungal tissues to the host plant are not well understood. ECM fungal isolates, even from the same species, vary considerably in their ability to support tree N nutrition resulting in a range of often unpredictable symbiotic outcomes. In this study, we used isotopic labelling to quantify the transfer of N to the plant host by isolates from the ECM genus Pisolithus known to have significant variability in colonisation and transfer of nutrients to a host. more...

Organism:

Eucalyptus grandis; Pisolithus microcarpus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33524 GPL33522 GPL33523

43 Samples

Download data: TXT

(Submitter supplied) Cryptococcus spp. are environmental fungi that first must adapt to the host environment before they can cause life-threatening meningitis in immunocompromised patients. Host CO2 concentrations are 100-fold higher than the external environment and strains unable to grow at host CO2 concentrations are not pathogenic. Using a genetic screening and transcriptional profiling approach, we found that the TOR pathway is critical for C. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21073

24 Samples

Download data: XLSX

(Submitter supplied) Isolates of Cryptococcus neoformans, a fungal pathogen that kills almost 200,000 people worldwide each year, differ at a few thousand up to almost a million DNA sequence positions compared to a 19-megabase reference genome. We used bulked segregant analysis and association analysis, genetic methods that require no prior knowledge of sequence function, to address the key question of which naturally occurring variants influence fungal virulence. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27451

16 Samples

Download data: CSV

(Submitter supplied) Phaffia rhodozyma is an ideal microbial astaxanthin resource. However, the low productivity of astaxanthin in this yeast obstructs the process of industrial production. Although P. rhodozyma is isolated from plant material and the phytohormone has proved to be an effective stimulator for microbial production, the effects and mechanisms of phytohormones on astaxanthin synthesis in P. rhodozyma have been rarely reported. more...

Organism:

Phaffia rhodozyma

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28708

6 Samples

Download data: XLSX

(Submitter supplied) To determine the wood degradation mechanism and its key genes of Lenzites gibbosa, we sequenced 15 transcriptomes of mycelial samples under woody environments at 3, 5, 7, and 11 d (D3, D5, D7, and D11) and non-woody environments (CK). All the transcripts were annotated as much as possible in eight databases to determine their function. The key genes and biological processes, relating to wood degradation, were predicted and screened. more...

Organism:

Trametes gibbosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30651

15 Samples

Download data: GFF, TXT

(Submitter supplied) Insufficient biosynthesis efficiency can be a major obstacle to engineer oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs) during the lipogenic phase. Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic preferences of three plant-derived ketoacyl-CoA synthases rationally guided reconstructing efficient NA biosynthetic pathway in R. more...

Organism:

Rhodotorula toruloides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32811

18 Samples

Download data: TXT

(Submitter supplied) The differential expression of the high-yield astaxanthin Phaffia rhodozyma BPAX-A1 with the wild-type Phaffia rhodozyma CBS6938 was obtained and analysed to understand metabolic changes leading to an improved astaxanthin production.

Organism:

Phaffia rhodozyma

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28708

6 Samples

Download data: XLSX