GEO DataSets

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

Organism:

Candida albicans x Candida dubliniensis; Candida albicans; Candida parapsilosis; Candida tropicalis; Candida dubliniensis

Type:

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

11 related Platforms

127 Samples

Download data: GPR, TXT

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different growth media. Ndt80 was tagged with a c-myc epitope in the three species and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain in two different media for each species.

Organism:

Candida tropicalis; Candida albicans; Candida dubliniensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL29382 GPL19036 GPL29383

24 Samples

Download data: TXT

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation. C. albicans or C. dubliniensis Ndt80 was tagged with a c-myc epitope in a C. albicans x C. dubliniensis hybrid and the immunoprecipitation of the tagged strain was compared to that of an untagged control hybrid strain.

Organism:

Candida albicans x Candida dubliniensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29384

6 Samples

Download data: TXT

(Submitter supplied) The purpose of this experiment was to identify the genes bound by the biofilm master regulators (Bcr1, Brg1, Efg1, Ndt80, Rob1 and Tec2) in Candida albicans, C. dubliniensis, C. tropicalis and C. parapsilosis during biofilm formation. The regulators were tagged with a c-myc epitope and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain.

Organism:

Candida tropicalis; Candida albicans; Candida parapsilosis; Candida dubliniensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

61 Samples

Download data: TXT

(Submitter supplied) The goal was to identify genes that change their expression in biofilm vs. planktonic growth. Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose, Spider and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL16243

12 Samples

Download data: GPR

(Submitter supplied) The goal was to identify genes that change their expression in biofilm vs. planktonic growth. Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and Spider. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL13813

8 Samples

Download data: GPR

(Submitter supplied) The goal was to identify genes that change their expression in biofilm vs. planktonic growth. Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. more...

Organism:

Candida tropicalis

Type:

Expression profiling by array

Platform:

GPL29364

8 Samples

Download data: GPR

(Submitter supplied) The goal was to identify genes that change their expression in biofilm vs. planktonic growth. Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and Spider. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. more...

Organism:

Candida dubliniensis

Type:

Expression profiling by array

Platform:

GPL29363

8 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) 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) 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) 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) 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) 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) 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) LYS142, LYS143, LYS14 and LYS144 compose a family of recently duplicated transcription regulators in C. albicans. They have differentiated from one another by acquiring a largely separate set of target genes. Chromatin immunoprecipitation (ChIP) of GFP-LYS142, GFP-LYS143, GFP-LYS14 and GFP-LYS144 followed by array hybridization (Agilent) uncovered a network of target genes controlled by these regulators in the yeast C. more...

Organism:

Candida albicans

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL17892

5 Samples

Download data: GPR

(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