GEO DataSets

(Submitter supplied) Purpose: Compare the fluconazole-induced transcriptome of isogenic wild-type and upc2A null cells. Methods: Prepare total RNA from wild-type and upc2A null cells grown under unstressed conditions or challenged with 50 microgram/ml fluconazole for 6 hours. Use standard RNA-seq to evaluate and compare the transcriptomic changes caused by fluconazole in the presence or absence of UPC2A. Results: These data established that over 100 genes were induced by fluconazole in a UPC2A-dependent manner. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22622

12 Samples

Download data: WIG

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

Organism:

Nakaseomyces glabratus; Nakaseomyces glabratus CBS 138

Type:

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

Platforms:

GPL30531 GPL22622

28 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Purpose: Determine the number of genes that respond to the presence of a gain-of-function mutant form of the UPC2A transcription factor in Candida glabrata. Methods: Prepare total RNA from wild-type and gain-of-function G898D UPC2A cells. Use standard RNA-seq to evaluate and compare the transcriptomic changes caused by this allele of UPC2A. Results: Although a clear increase was seen in fluconazole resistance conferred by the G898D UPC2A allele, elevated transcription was only observed for 11 genes with 9 of these involved in ergosterol biosynthesis. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22622

6 Samples

Download data: BIGWIG

(Submitter supplied) To determine the genomic binding sites for the Candida glabrata transcription factor Upc2A, we utilized three different strains. One was the wild-type KKY2001 which contains a wild-type copy of UPC2A but lacks any HA tag. The other two are both derived from KKY2001 but contain a 3X HA tag immediately after the start codon of UPC2A. These strains are BVGC82 and BVGC84, respectively. Both contain a single copy of a loxP element located 252 bp downstream from the UPC2A stop codon. more...

Organism:

Nakaseomyces glabratus CBS 138

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30531

10 Samples

Download data: WIG

(Submitter supplied) Two of the major classes of antifungal drugs in clinical use target ergosterol biosynthesis. Despite its importance, our understanding of the transcriptional regulation of ergosterol biosynthesis genes in pathogenic fungi is essentially limited to the role of hypoxia and sterol-stress induced transcription factors such as Upc2 and Upc2A as well as homologs of Sterol Response Element Binding (SREB) factors. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31108

25 Samples

Download data: XLSX

(Submitter supplied) Pdr1 is the major regulator of azole resistance in the fungal pathogen Candida glabrata. Earlier experiments demonstrated that expression of Pdr1 itself is increased when cells lose their mitochondrial genome (rho0). Here we use chromatin immunoprecipitation coupled with highthroughput sequencing (ChIP-seq) to map the genomic binding sites for Pdr1 in both normal and rho0 cells. These data provide the first look at genes that are likely to represent the direct targets of Pdr1 in this important pathogen.

Organism:

Nakaseomyces glabratus CBS 138

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19002

9 Samples

Download data: WIG

(Submitter supplied) The opportunistic yeast pathogen Candida glabrata is recognized for its ability to acquire resistance during prolonged treatment with azole antifungals. Resistance to azoles is largely mediated by the transcription factor PDR1, resulting in the upregulation of ATP-binding cassette (ABC) transporter proteins and drug efflux. Studies in the related yeast Saccharomyces cerevisiae have shown Pdr1p forms a heterodimer with another transcription factor, Stb5p. more...

Organism:

Nakaseomyces glabratus; Nakaseomyces glabratus CBS 138

Type:

Expression profiling by array

Platforms:

GPL8174 GPL10325

13 Samples

Download data: GPR, TXT

(Submitter supplied) Eukaryotic transcription activators stimulate the expression of specific sets of target genes through recruitment of co-activators such as the RNA polymerase II-interacting Mediator complex. We previously identified an activator-targeted ~85 amino acid three-helix bundle KIX domain in the human MED15 Mediator subunit that is structurally conserved in Gal11 Mediator subunits in fungi. The Gal11 KIX domain is engaged by pleiotropic drug resistance transcription factor (Pdr1) orthologues, key regulators of the multidrug resistance (MDR) pathway in S. more...

Organism:

Nakaseomyces glabratus; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL21066

24 Samples

Download data: TXT

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

Organism:

Nakaseomyces glabratus CBS 138; Nakaseomyces glabratus

Type:

Expression profiling by array

Platform:

GPL10713

33 Samples

Download data: TXT

(Submitter supplied) In this study, we aimed to determine genome-wide changes in gene expression driven by seven individual CgPDR1 hyperactive alleles as compared to wild-type allele to identify i) the CgPdr1p target genes differentially expressed in presence of CgPDR1 hyperactive alleles and ii) potential virulence factor(s) regulated by CgPDR1 hyperactive alleles. Microarray experiments revealed a high number of genes (ranging from 80 to 400 genes) differentially regulated by individual CgPDR1 hyperactive alleles.

Organism:

Nakaseomyces glabratus; Nakaseomyces glabratus CBS 138

Type:

Expression profiling by array

Platform:

GPL10713

6 Samples

Download data: TXT

(Submitter supplied) In this study, we aimed to determine genome-wide changes in gene expression driven by seven individual CgPDR1 hyperactive alleles as compared to wild-type allele to identify i) the CgPdr1p target genes differentially expressed in presence of CgPDR1 hyperactive alleles and ii) potential virulence factor(s) regulated by CgPDR1 hyperactive alleles. Microarray experiments revealed a high number of genes (ranging from 80 to 400 genes) differentially regulated by individual CgPDR1 hyperactive alleles.

Organism:

Nakaseomyces glabratus CBS 138; Nakaseomyces glabratus

Type:

Expression profiling by array

Platform:

GPL10713

27 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to compare C. glabrata transcriptome profiling (RNA-seq) upon exposure to the antifungal fluconazole in order to assess antifungal response. The role of the transcription factor Rpn4 is clarified through comparison of the transcrptome profiles of WT and Rpn4 mutant cells. mRNA profiles of WT and ∆rpn4 were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq. RNA-seq data allowed to identify genes whose expression is regulated by the Rpn4 transcription factor (80 positively regulated and 212 negatively regulated) with a log2fold change ≥0.5 and p value <0.05. The transcriptomics data was then used to guide further work to detail the function of Rpn4.

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26394

8 Samples

Download data: TXT

(Submitter supplied) The pathogenic yeast species Candida glabrata has an intrinsically high resilience to azoles and a rapid capability of acquiring resistance. Azole-resistant clinical strains derive mostly from them encoding hyperactive mutants of the CgPdr1 regulator, however, strains encoding wild-type CgPdr1 variants were identified suggesting a role for CgPdr1-independent mechanisms in acquisition of resistance in vivo. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by array

Platform:

GPL29725

14 Samples

Download data: TXT, XLS

(Submitter supplied) To determine the effect of caspofungin (CSP) treatment and/or loss of the SET domain-containing CgSet4 protein on the transcriptional response of log-phase C. glabrata cells. RNA-Seq analysis was conducted on CAA medium-grown log-phase Candida glabrata wild-type (wt) and CgSET4-deleted (Cgset4D) cells in the presence and absence of caspofungin.

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25492

8 Samples

Download data: XLSX

(Submitter supplied) This study investigated the effect of milbemycons as efflux inhibitors and antifungal agents. Milbemycin oxims can inhibit growth of Candida glabrata and C. albicans. The effect of milbemycins on transcriptomes was inbvestigated.

Organism:

Nakaseomyces glabratus CBS 138; Candida albicans; Nakaseomyces glabratus

Type:

Expression profiling by array

Platforms:

GPL10713 GPL15960

14 Samples

Download data: TXT

(Submitter supplied) Microarray was used to analyze azole resistance of Candida glabrata oropharyngeal isolates from 7 hematopoietic stem cell transplant recipients receiving fluconazole prophylaxis. Transcriptional profiling of the sequential-paired clinical isolates by microarray revealed 19 genes upregulated in the majority of resistant isolates compared to their paired-susceptible isolates. All seven resistant isolates had greater than two fold upregulation of CgPDR1, a master transcriptional regulator of PDR network, and all 7 resistant isolates showed upregulation of known CgPDR1-target genes. more...

Organism:

Nakaseomyces glabratus CBS 138; Nakaseomyces glabratus

Type:

Expression profiling by array

Platform:

GPL10325

8 Samples

Download data: TXT

(Submitter supplied) Microarray was used to analyze azole resistance of Candida glabrata oropharyngeal isolates from 7 hematopoietic stem cell transplant recipients receiving fluconazole prophylaxis. Transcriptional profiling of the sequential-paired clinical isolates by microarray revealed 19 genes upregulated in the majority of resistant isolates compared to their paired-susceptible isolates. All seven resistant isolates had greater than two fold upregulation of CgPDR1, a master transcriptional regulator of PDR network, and all 7 resistant isolates showed upregulation of known CgPDR1-target genes. more...

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by array

Platform:

GPL8174

35 Samples

Download data: GPR

(Submitter supplied) In the present study the gene encoding the putative J protein Jjj1 was deleted in a susceptible dose dependent clinical isolate resulting in decreased susceptibility to fluconazole compared to wild type. When JJJ1 was deleted in combination with the transcription factor PDR1 the fluconazole susceptibility was consistently only one fold higher from the strain deleted for PDR1 alone. Expression profiling was conducted to determine which genes have altered expression in the absence of JJJ1 and which of these alterations are dependent on PDR1 expression.

Organism:

Nakaseomyces glabratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24070

6 Samples

Download data: TXT, XLSX

(Submitter supplied) In the pathogenic yeast Candida albicans, the zinc cluster transcription factor Upc2p has been shown to regulate expression of ERG11 and other genes involved in ergosterol biosynthesis upon exposure to azole antifungals. ERG11 encodes lanosterol demethylase, the target enzyme of this antifungal class. Over-expression of UPC2 reduces azole susceptibility, whereas its disruption results in hypersusceptibility to azoles and reduced accumulation of exogenous sterols. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platforms:

GPL5723 GPL6808

18 Samples

Download data: CEL, CHP

(Submitter supplied) Two C. glabrata related isolates recovered from the same patient undergoing azole therapy were characterized. The first isolate, BPY40, is azole-susceptibleand the second, BPY41, is azole-resistant. To determine whether the petite mutation conferred a selective advantage during host infection, the virulence of BPY40 and BPY41 was assessed in mice. Surprisingly, the petite mutant, even if showing in vitro growth deficiency as compared to BPY40, was more virulent than BPY40 both in intravenous and vaginal murine infection models. more...

Organism:

Nakaseomyces glabratus; Nakaseomyces glabratus CBS 138

Type:

Expression profiling by array

Platform:

GPL10713

6 Samples

Download data: TXT