GEO DataSets

(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) 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) Candida albicans is the most common opportunistic fungal pathogen of humans and is also a benign member of the gastrointestinal (GI) tract microbiota. Morphological transitions and metabolic regulation are critical for C. albicans to adapt to the changing host environment. We generated a library of central metabolic pathway mutants in the tricarboxylic acid (TCA) cycle, and investigated the functional consequences of these gene deletions on C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15645

8 Samples

Download data: XLS

(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) 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) 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) Biofilms are sessile microbial communities that are often resistant to conventional antimicrobial therapeutics and the host immune system. Candida albicans is an opportunistic pathogenic yeast and responsible for candidiasis. It readily colonizes host tissues and implant devices, and forms biofilms, which play an important role in pathogenesis and drug resistance. Its morphological transition from budding yeast to hyphal form and subsequent biofilm formation is regarded as the crucial factor for drug tolerance and virulence of Candida infections. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19036

2 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) 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) 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) Similar to S. cerevisiae Rta1 (role in 7-aminocholesterol resistance) and Rsb1 (flippase); putative drug-responsive regulatory site; induced by fluphenazine, estradiol, ketoconazole, caspofungin; rat catheter biofilm induced

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL21450

6 Samples

Download data: TXT

(Submitter supplied) The polymorphic yeast Candida albicans exists in blastospore and filamentous forms. The switch from one morphological state to the other coincides with the expression of virulence factors, which makes the yeast-to-hypha transition an attractive target for the development of new antifungal agents. Because an untapped therapeutic potential resides in small molecules that hinder C. albicans filamentation, we characterized the inhibitory effect of conjugated linoleic acid (CLA) on hyphal growth and addressed its mechanism of action. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL9818

12 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

(Submitter supplied) To elucidate the impact of IFU5 in Candida albicans, genome wide transcription profiling was performed in ifu5?/? mutant strain. Wild type and mutant cells were grown for 5 hours and RNA extracted from these cultures, followed by microarray profiling. Expression of six genes (EFG1, ALS3, SOD3, BMT4, COX2, NAD1) was validated by qPCR.

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL21450

4 Samples

Download data: TXT

(Submitter supplied) The Zap1 ChIP-chips were performed in a/alpha cell types using C-terminally Myc-tagged proteins and Myc antibodies. ChIPs were performed on 48 hour biofilm cells grown in Spider medium. Two biological replicates were performed, and normalized data is reported in matrix.

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13696

4 Samples

Download data: GPR

(Submitter supplied) The planktonic versus biofilm gene expression arrays were performed in a/alpha cell types. Gene expression arrays were performed on planktonic vs biofilm cells grown in Spider medium at 37C. Normalized data is reported in matrix.

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL13830

2 Samples

Download data: GPR

(Submitter supplied) The purpose of this experiment was to identify the genes with increased expression during sporulation in wild-type P. pastoris, and during sporulation in cells with Ndt80 deleted. Cells were grown unti log-phase in YPD or in sporulation media (0.5% sodium acetate, 1% potassium chloride, 1% glucose, 2% agar plates ) for 30 hours. Each experiment was repeated three times and sequenced on an Illumina HiSeq 4000

Organism:

Komagataella pastoris

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22717 GPL22842

9 Samples

Download data: GTF

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the two Ndt80 paralogs in C. albicans when constitutively expressed, and for Ndt80B when endogenously expressed. Both paralogs were tagged with c-myc, and the protein was immunoprecipitated with a c-myc antibody. For constitutive expression, each native Ndt80 promoter was replaced by the C. albicans Tdh3 promoter. Cells were grown unti log-phase in YPD. more...

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19036

8 Samples

Download data: WIG, XLS