GEO DataSets

(Submitter supplied) Candida albicans can stochastically switch between two phenotypes, white and opaque. Opaque cells are the sexually competent form of C. albicans and therefore undergo efficient polarized growth and mating in the presence of pheromone. In contrast, white cells cannot mate, but are induced - under a specialized set of conditions - to form biofilms in response to pheromone. In this work, we compare the genetic regulation of such "pheromone-stimulated" biofilms with that of "conventional" C. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL16385

17 Samples

Download data: GPR

(Submitter supplied) C. albicans is a dimorphic yeast which can switch from budding yeast and to hyphal forms and this property is essential for biofilm establishment and maturation. C. albicans undergoes this yeast-to-hyphal switch in response to high CO2. The purpose of this study is to use RNA-seq to investigate pathways whose genes are differentially expressed when C. albicans biofilms are grown in a physiologically relevant elevated (5%) CO2 environment compared to a low/atmospheric (0.03%) CO2 environment. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22403

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The capacity of the commensal yeast Candida albicans to grow in several forms, referred to as phenotypic plasticity, is critical for its survival, and abilities to thrive and cause infection in the human host. In this study, we report a novel phenotype of C. albicans, referred as the “gray” phenotype. The gray cell type, together with the previously discovered “white” and “opaque” cell types, forms a tristable phenotypic switching system. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15645

3 Samples

Download data: TXT

(Submitter supplied) Modes of sexual reproduction in eukaryotic organisms are highly diversified. The human fungal pathogen Candida albicans undergoes a phenotypic switch from the white to the opaque phase in order to become mating-competent. In this study, we report that functionally and morphologically differentiated white and opaque cells show a coordinating behavior in the process of mating. Although white cells are mating-incompetent, they are induced to produce sexual pheromones when treated with opposite pheromones or interacted with opaque cells of an opposite mating type. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15645

2 Samples

Download data: TXT

(Submitter supplied) Twenty-one pheromone-induced genes were selected from the literature (Zhao, Daniels et al. 2005 was the major source) as the reference set for assessing the pheromone response of CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains.Our aim was to check whether or not these 21 pheromone-induced genes are up-regulated in response to pheromone in each mutant strain.

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23041

28 Samples

Download data: TSV, XLSX

(Submitter supplied) To understand the biological relevance of the role played by the HHT1 histone H3 variant in C. albicans, we performed a transcriptome analysis of the mutant by global gene expression array analysis. We analyzed gene expression profile of the mutant in strains LR107 and LR108 (hht1∆/hht1∆) and the parent wild type (SC5314) strain grown in YPD liquid medium at 30°C. In the microarray analysis, a total of 1222 genes were found to be expressed significantly different (fold change < 1.5 at p-value < 0.05) between wild type and two hht1 null mutants. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL20624

8 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of a-type wor1 deleted cells and mixed a-type and alpha-type opaque cells under in vitro biofilm-forming conditions. Specifically, they were grown for two days at room temperature in a 12-well poly-styrene plate containing 1 ml of Lee's + Glucose liquid media. Samples were hybridized against a universal mixed reference sample of a-type cells in white and opaque states grown in Spider liquid media.

Organism:

Candida tropicalis

Type:

Expression profiling by array

Platform:

GPL15925

4 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. tropicalis a cells (CAY1503) in opaque state and overexpressing Wor1 in biofilms hybridized against a universal mixed reference sample of a cells in white and opaque states grown in Spider liquid.

Organism:

Candida tropicalis

Type:

Expression profiling by array

Platform:

GPL15925

4 Samples

Download data: GPR

(Submitter supplied) Abstract: Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CUG clade in the Saccharomycotina. In contrast to C. albicans, relatively little is known about the virulence properties of C. parapsilosis, a pathogen particularly associated with infections of premature neonates. We describe here the construction of >200 C. parapsilosis strains carrying double allele deletions of transcription factors, protein kinases and species-specific genes. more...

Organism:

Candida parapsilosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18663

24 Samples

Download data: TXT

(Submitter supplied) Candida albicans is an opportunistic fungal pathogen that can infect oral mucosal surfaces despite being under continuous flow from saliva. Previous studies have shown that under specific conditions C. albicans will form microcolonies that more closely resemble the biofilms formed in vivo than standard in vitro biofilm models. However, very little is known about these microcolonies, particularly genomic differences between these specialized biofilm structures and the traditional in vitro biofilms. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19036

6 Samples

Download data: DIFF

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

Organism:

Candida parapsilosis

Type:

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

Platform:

GPL16091

14 Samples

Download data

(Submitter supplied) In Candida albicans the Efg1 transcription factor (a member of the APSES family) is an important regulator of hyphal growth, and of the white-to-opaque transition. In contrast, we show that the Efg1 ortholog in Candida parapsilosis is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 100-fold increased in an efg1 knockout relative to wild type. more...

Organism:

Candida parapsilosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16091

8 Samples

Download data: TXT

(Submitter supplied) We use ChIP-seq to identify the targets of Efg1 in Candida parapsilosis. We show that Efg1 binds to 502 promoter regions, including 70 potential transcription factors or regulatory proteins. Several of the transcription factors belong to networks that regulate biofilm development and white-opaque switching in C. albicans. Efg1 also binds to its own promoter. The binding site for C. parapsilosis Efg1 resembles that of orthologs in other fungi. more...

Organism:

Candida parapsilosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16091

6 Samples

Download data: FASTA, TXT

(Submitter supplied) Transcriptional profiling of Candida albicans cells grown under planktonic and biofilm-inducing conditions, comparing SN76 and sfl1Δ/sfl1Δ strains. Goal was to study the effect of SFL1 deletion on the transcriptomic profile of C. albicans planktonic and biofilm cells under acidic conditions, in order to reveal the function of the Sfl1 transcription factor in C. albicans biofilm development.

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL22275

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of C. albicans in biofilms after 90 min of adherence or 8 h, 24 h, or 48 h of development; compared to C. albicans in suspension cultures grown to log at 30 deg or 37 deg or grown to stationary phase at 30 deg or collected from the unadhered cells in the biofilm assay.

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL13830

29 Samples

Download data: GPR, TIFF, TXT

(Submitter supplied) To delineate the functional role of ZCF32 in Candida albicans biology, we carried out the genome wide expression analysis of wild-type and zcf32 null mutants by global expression array. We analysed the gene expression profiles of YPK102/1 and YPK102/2 and the parent wild type (SC5314) strain grown in YPD liquid medium at 30°C till the start of the stationary phase. In the microarray analysis, a total of 607 genes were found to be differentially expressed (fold change < 1.5 at p-value < 0.05) between the wild type and two zcf32 null mutants. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL21258

4 Samples

Download data: TXT

(Submitter supplied) The Poly(A)-Tail focused RNA-seq, or PAT-seq approach, is an affordable and efficient tool for the measure of 3’UTR dynamics. We show here that PAT-seq returns (i) digital gene expression, (ii) polyadenylation site usage within and between samples, including alternative adenylation, and (iii) the polyadenylation-state the transcriptome. PAT-seq differs from previous 3’ focused RNA-seq methods in that it strictly depends on native 3’ adenylation within total RNA samples and thus removes the need for ribosome depletion and, that the full native poly(A)-tail is included in the sequencing libraries. more...

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18085

13 Samples

Download data: CSV

(Submitter supplied) It has been proposed that the ancestral fungus was mating competent and homothallic. However, many mating competent fungi were initially classified as asexual because their mating capacity was hidden behind layers of regulation. For efficient in vitro mating, the essentially obligate diploid ascomycete pathogen C. albicans has to homozygose its mating type locus from MTLa/α to MTLa/a or MTLα/α, and then undergo an environmentally controlled epigenetic switch to the mating competent opaque form. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL19196

9 Samples

Download data: TXT

(Submitter supplied) The discovery of white-opaque switching in natural MTLa/alpha isolates of Candida albicans sheds new light on the evolution of phenotypic plasticity and host adaptation.

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15645

2 Samples

Download data: TXT

(Submitter supplied) The ability of the fungus Candida albicans to filament and form biofilms contributes to its burden as a leading cause of hospital-acquired infections. Biofilm development involves an interconnected transcriptional regulatory network (TRN) consisting of nine transcription factors (TFs) that bind both to their own regulatory regions and to those of the other network TFs. Here, we show that seven of the nine TFs in the C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28323

12 Samples

Download data: CSV, TXT