GEO DataSets

(Submitter supplied) Cryptococcus neoformans is a ubiquitous free-living soil yeast and opportunistic pathogen that causes ~223,100 cases of cryptococcal meningitis per year, killing over 180,000 people. The pathogenicity of C. neoformans relies on its adaptation to the host conditions. An important difference between its natural environment and the mammalian host is the concentration of CO2. CO2 levels in the host fluctuate around 5%, which is ~125-fold higher than in ambient air. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21073

18 Samples

Download data: XLSX

(Submitter supplied) Purpose: To examine the comparative transcriptional profiles of WT and rim101 mutant cells in host-mimicking in vitro conditions to determine genes that are responsible for the increased virulence of the rim101 strain. The rim101 mutant is able to trigger an overactive inflammatory response, presumably by exposing an antigenic trigger. Using transcriptional profiling, we determined that many genes involved in cell wall processes were differentially transcribed between the wild type and the mutant strain.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16431

2 Samples

Download data: CSV

(Submitter supplied) We report on our study the role of C. neoformans transcription factor Pdr802, whose expression is highly induced under host-like conditions in vitro and is critical for C. neoformans dissemination and virulence in a mouse model of infection. We found that direct targets of Pdr802 include the calcineurin targets Had1 and Pmc1, which are important for C. neoformans virulence, the transcription factor Bzp4, which promotes cryptococcal melanization and capsule thickness, and 35 transmembrane transporters. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27451

56 Samples

Download data: CSV

(Submitter supplied) We report on our study the role of C. neoformans transcription factor Pdr802, whose expression is highly induced under host-like conditions in vitro and is critical for C. neoformans dissemination and virulence in a mouse model of infection. We found that direct targets of Pdr802 include the calcineurin targets Had1 and Pmc1, which are important for C. neoformans virulence, the transcription factor Bzp4, which promotes cryptococcal melanization and capsule thickness, and 35 transmembrane transporters. more...

Organism:

Cryptococcus neoformans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27451

12 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) The transcriptional responses of cryptococcus during human infection are dynamic and highly dependent on the immediate signals from the environment. We examined the RNA-Seq profiles of Cryptococcus isoalted from human CSF and in comparison with to the same isolate's response to the stresses of artificial CSF and within the rabbit subarachnoid space as well as growth in nutritious media with little or no stress. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19081 GPL27451

125 Samples

Download data: TXT

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen responsible for hundreds of thousands of deaths per year. Its critical virulence factor is a polysacharride capsule which grows large upon entry into a mammalian host. We previously identified USV101 as a transcription factor whose deletion results in enlarged capsules. Here, we characterize strains lacking or overexpressing USV101 in terms of their virulence-related phenotypes, the altered course of infection by them and immune response to them in a mouse model, the relationship of Usv101 to other transcription factors involved in capsule regulation, and the changes in Usv101 activity during capsule induction.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19081

46 Samples

Download data: CUFF, TXT

(Submitter supplied) Purpose: Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying TFs involved in a specific process and used it to map regulation of the key virulence factor of Cryptococcus neoformans, its capsule. Results: The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. more...

Organism:

Cryptococcus neoformans

Type:

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

Platforms:

GPL19081 GPL14571

320 Samples

Download data: BED, CUFF, TXT

(Submitter supplied) Candida albicans is a commensal yeast of the human gut, which is tolerated by the immune system, but has the potential to become an opportunistic pathogen. One way in which C. albicans achieves this duality is through the concealing, or exposure of cell wall associated pathogen-associated molecular patterns (PAMPs) in response to host derived environment cues (pH, hypoxia, lactate). This cell wall remodelling allows C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24129

33 Samples

Download data: XLSX

(Submitter supplied) Cryptococcus neoformans is an opportunistic basidiomycete pathogen that is a major etiological agent of fungal meningoencephalitis leading to more than 180,000 deaths worldwide annually. For this pathogen, the polysaccharide capsule is a key virulence factor, which interferes with the phagocytosis by host innate immune cells, but its complex signaling networks remain elusive. In this study, we systematically analyzed capsule biosynthesis and signaling networks by using C. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32481

30 Samples

Download data: XLSX

(Submitter supplied) Cryptococcus neoformans is an important pathogen that annually kills 200,000 people worldwide. It survives in the environment as a yeast or spore and can also proliferate within host macrophages after being inhaled into the lungs. In conditions of immunocompromise, cryptococcal cells can escape from the lungs to the brain, where they cause a deadly meningoencephalitis that is both difficult and expensive to treat. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19081

21 Samples

Download data: TSV

(Submitter supplied) In eukaryotes, inositol polyphosphates perform essential metabolic and signaling functions. Using human fungal pathogen Cryptococcus neoformans as a model, we created mutants in three inositol polyphosphates kinases: Arg1, Ipk1 and Kcs1. Each of the mutants produces a unique repertoire of inositol polyphosphates, different from the wild type strain. Comparative phenotypic and transcriptome analyses of wild type and mutant strains indicates that inositol polyphosphate PP-IP5 (IP7) is the key regulator of gene expression, fitness and virulence in C. more...

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21548

12 Samples

Download data: TAB

(Submitter supplied) To determine how the fungal sterol homeostasis pathway contributes to the fungal pH response. To do so, we compared the transcriptomes of the sre1∆ mutant strain to that of the WT H99 strain in acidic (pH 4) and alkaline (pH 8) conditions.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27451

24 Samples

Download data: TXT

(Submitter supplied) The basidiomycete fungus Ustilago maydis causes smut disease in maize and has become an important model for elucidating the strategies used for host colonization by biotrophic fungi. In this study, we performed an in-depth transcriptional profiling of the plant-associated development of a cross between U. maydis FB1 and FB2 wildtype strains. The analysis of eight different stages, including the development on the leaf surface, early colonization, tumor induction and spore maturation, offers an unprecedented view of the changes in the fungal transcriptome associated with the passage through the entirely biotrophic life cycle. more...

Organism:

Zea mays; Mycosarcoma maydis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19655 GPL24015 GPL15463

45 Samples

Download data: TXT

(Submitter supplied) Purpose: To identify the downstream gene sets regulated by Mpk1p in C. neoformans normal and Tunicamycin-treated conditions, we compared the RNA-seq based transcriptional profiles. Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and all procedure for RNA sequencing were conducted by ebiogen. The mRNA was isolated by using the Poly(A) RNA Selection Kit (LEXOGEN) and isolated mRNAs were used for the cDNA synthesis. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28713

8 Samples

Download data: XLSX

(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) We wanted to find out the transcriptomic response of growth arrested wild type (KN99α) and Gat201 deletion mutant Cryptococcus yeast cells reactivating in cell culture media with and without serum.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32829

56 Samples

Download data: TXT

(Submitter supplied) We wanted to find out the transcriptomic response of growth-arrested Cryptococcus yeast cells when initially placed in environments in which they could reactivate or "wake up", focusing on the difference between a rich microbial media (YPD) and a common cell culture media, RPMI + 10% heat-inactivated fetal calf serum. Please contact [email protected] if you use this data and ask for citation information; we are currently (August 2020) working on a publication.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24689

36 Samples

Download data: TXT