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Links from GEO DataSets

Items: 18

1.

Species- and condition-specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis

(Submitter supplied) Although Candida albicans and Candida dubliniensis are most closely related, both species significantly behave differently with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for C. albicans and C. dubliniensis, respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for C. albicans and C. dubliniensis confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for C. albicans and C. dubliniensis, respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in C. albicans. Species specific adaptation in C. albicans and C. dubliniensis is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level.
Organism:
Candida dubliniensis; Candida albicans
Type:
Expression profiling by high throughput sequencing
6 related Platforms
14 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE41749
ID:
200041749
2.

Expression profiling of Candida albicans and Candida dubliniensis in reconstituted human oral epithelium 90 min p.i.

(Submitter supplied) Candida albicans and Candida dubliniensis are closely related species displaying differences in virulence and genome content, therefore providing potential opportunities to identify novel C. albicans virulence genes. C. albicans gene arrays were used for comparative analysis of global gene expression in the two species in reconstituted human oral epithelium (RHE). C. albicans (SC5314) showed upregulation of hypha-specific and virulence genes within 30 min postinoculation, coinciding with rapid induction of filamentation and increased RHE damage. more...
Organism:
Candida albicans; Candida dubliniensis
Type:
Expression profiling by array
Platform:
GPL6453
8 Samples
Download data: GPR, TXT
Series
Accession:
GSE13345
ID:
200013345
3.

Expression profiling of Candida albicans and Candida dubliniensis in reconstituted human oral epithelium 30 min p.i.

(Submitter supplied) Candida albicans and Candida dubliniensis are closely related species displaying differences in virulence and genome content, therefore providing potential opportunities to identify novel C. albicans virulence genes. C. albicans gene arrays were used for comparative analysis of global gene expression in the two species in reconstituted human oral epithelium (RHE). C. albicans (SC5314) showed upregulation of hypha-specific and virulence genes within 30 min postinoculation, coinciding with rapid induction of filamentation and increased RHE damage. more...
Organism:
Candida dubliniensis; Candida albicans
Type:
Expression profiling by array
Platform:
GPL6475
6 Samples
Download data: GPR, TXT
Series
Accession:
GSE13318
ID:
200013318
4.

Transcriptional response of Candida dubliniensis during hypha formation and environmental change

(Submitter supplied) Transcriptional response of Candida dubliniensis during hypha formation and environmental change (temperature, pH, density and nutrients). Transcript profiling of C. dubliniensis identified a core shared transcriptional response with C. albicans during hypha formation and growth at alkaline pH. However, C. albicans expresses several unique hypha-specific genes, including ALS3, HYR1 and SAP4 and 5. Transcript profiling also revealed a novel role for NRG1 in regulating ferric reductases in C. more...
Organism:
Candida dubliniensis
Type:
Expression profiling by array
Platform:
GPL10110
32 Samples
Download data: GPR
Series
Accession:
GSE20537
ID:
200020537
5.

Transcriptional profiling and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans

(Submitter supplied) Invasion of host tissue by the human fungal pathogen, Candida albicans is an important step during many forms of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. It is known for example that the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade into host tissue and to cause infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence as compared to SC5314. more...
Organism:
Candida albicans
Type:
Genome variation profiling by array
Platform:
GPL6453
2 Samples
Download data: GPR
Series
Accession:
GSE10689
ID:
200010689
6.

A family of secreted pathogenesis-related proteins in Candida albicans

(Submitter supplied) Analyzing culture supernatants of yeast and hyphal cells of Candida albicans by mass spectrometry, we found two close homologues of pathogenesis-related (PR-) 1 proteins, Rbe1p and Rbt4p, in the secretome of this human pathogen. By sequence homology, we assigned three yet not characterized open reading frames, ORF19.6200, ORF19.2787 and ORF19.2336, in addition to Rbe1p and Rbt4p to a novel family of proteins. more...
Organism:
Candida albicans; Candida albicans SC5314
Type:
Expression profiling by array
Platform:
GPL10374
12 Samples
Download data: GPR
Series
Accession:
GSE28212
ID:
200028212
7.

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high resolution tiling arrays

(Submitter supplied) Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. Here we have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. more...
Organism:
Candida albicans
Type:
Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL10636 GPL10637
12 Samples
Download data: TXT
Series
Accession:
GSE22625
ID:
200022625
8.

Comparative Genome Hybridization between Candida albicans and Candida dubliniensis and their derivatives

(Submitter supplied) Total genomic DNAs of J118, CdUM4b, the pseudotetraploid hybrid strain HBT1 and the progeny hybrid strain HBP1 were isolated. In an attempt to determine the number of copies of individual chromosomes, we used comparative genome hybridization (CGH) analysis using specially designed whole genome microarrays representing C. albicans and C. dubliniensis genomes. The arrays contained 60 mer probes that fell in three categories either C. more...
Organism:
Candida albicans; Candida dubliniensis; Candida albicans x Candida dubliniensis
Type:
Genome variation profiling by genome tiling array
Platform:
GPL10949
4 Samples
Download data: TXT
Series
Accession:
GSE24269
ID:
200024269
9.

Transcriptional landscape of the pathogenic yeast Candida parapsilosis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Candida parapsilosis
Type:
Expression profiling by array; Expression profiling by high throughput sequencing
Platforms:
GPL13192 GPL14718
34 Samples
Download data: GPR, SAM
Series
Accession:
GSE32716
ID:
200032716
10.

Transcriptional landscape of Candida parapsilosis

(Submitter supplied) We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations.
Organism:
Candida parapsilosis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14718
26 Samples
Download data: SAM
Series
Accession:
GSE32714
ID:
200032714
11.

Transcriptional profile of Candida parapsilosis CLIB214 versus UPC2 delete, both at 1% oxygen (hypoxia)

(Submitter supplied) Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis UPC2 delete in hypoxia.
Organism:
Candida parapsilosis
Type:
Expression profiling by array
Platform:
GPL13192
4 Samples
Download data: GPR
Series
Accession:
GSE32713
ID:
200032713
12.

Transcriptional profile of Candida parapsilosis CLIB214 21% Oxygen (normoxia) versus at 1% oxygen (hypoxia).

(Submitter supplied) Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition.
Organism:
Candida parapsilosis
Type:
Expression profiling by array
Platform:
GPL13192
4 Samples
Download data: GPR
Series
Accession:
GSE32712
ID:
200032712
13.

Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans

(Submitter supplied) Though sequence differences between alleles are often limited to a few polymorphisms, these differences can cause large and widespread allelic variation at the expression level. Such allele-specific expression (ASE) has been extensively explored at the level of transcription but not translation. Here we measured ASE in the diploid yeast Candida albicans at both the transcriptional and translational levels using RNA-seq and ribosome profiling, respectively. more...
Organism:
Candida albicans
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL15149
2 Samples
Download data: WIG
14.

Defining the transcriptome landscape of Candida glabrata during pH change and nitrosative stress by RNA-Seq

(Submitter supplied) The yeast Candida glabrata is one of the most important human fungal pathogens and has emerged as a leading cause of nosocomial bloodstream infections. Its resistance to many routinely used antimycotics and its close relationship to the model organism Saccharomyces cerevisiae make this fungus an interesting target of biomedical research. Although the genome sequence was published a decade ago, little is known about the transcriptional dynamics within this pathogen, especially compared to other pathogenic and nonpathogenic yeasts.We provide a detailed RNA-Seq-based analysis of the transcriptomic landscape of C. more...
Organism:
[Candida] glabrata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19215
16 Samples
Download data: XLS
Series
Accession:
GSE61606
ID:
200061606
15.

The Transcriptional Stress Response of Candida albicans to Weak Organic Acids

(Submitter supplied) Candida albicans is the most important fungal pathogen of humans, causing severe infections especially in nosocomial and immunocompromised settings. However, it is also the most prevalent fungus of the normal human microbiome, where it shares its habitat with hundreds of trillions of other microbial cells. Despite weak organic acids (WOAs) being among the most abundant metabolites produced by bacterial microbiota, little is known about their effect on C. more...
Organism:
Candida albicans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL15645
96 Samples
Download data: RPKM
Series
Accession:
GSE49310
ID:
200049310
16.

Array CGH with DNA extracted from Candida albicans strains 3153A and its derivative Sor55, which is monosomic for chromosome 5

(Submitter supplied) Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the mutant Sor55
Organism:
Candida albicans
Type:
Genome variation profiling by genome tiling array
Platform:
GPL10372
3 Samples
Download data: PAIR, TXT
Series
Accession:
GSE21616
ID:
200021616
17.

Monosomic chr5 derivative of laboratory strain of Candida albicans 3153A

(Submitter supplied) Differential expression between monosoic derivative and parental strain of Candida albicans. The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, assuring survival. In the absence of the adverse environment, the altered portion of the genome can be restored to its normal condition. more...
Organism:
Candida albicans
Type:
Expression profiling by array
Platforms:
GPL9251 GPL9252
6 Samples
Download data: TXT
Series
Accession:
GSE18779
ID:
200018779
18.

Candida albicans: Control vs. sulfite-treated cells

(Submitter supplied) Transcriptional profiling of Candida albicans cells comparing control untreated C. albicans cells with sulfite-treated C. albicans cells. Sulfite is a toxic molecule that C. albicans encounters in its human host. Both wild type and ∆zcf2 mutant cells were used. The goal was to determine the effects of sulfite on C. albicans gene expression, and to determine which of the genes areZcf2-depedent.
Organism:
Candida albicans
Type:
Expression profiling by array
Platform:
GPL16243
8 Samples
Download data: TXT
Series
Accession:
GSE90819
ID:
200090819
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