GEO DataSets

(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 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 albicans; Candida parapsilosis; Candida dubliniensis; Candida tropicalis

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

61 Samples

Download data: TXT

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

Organism:

Candida tropicalis; Candida albicans; Candida parapsilosis; Candida dubliniensis; Candida albicans x 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 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) Biofilm formation on medically implanted devices by Candida albicans poses a significant clinical challenge. Here we compared biofilm-associated gene expression in two clinical C. albicans isolates, SC5314 and WO-1, to identify shared gene regulatory responses that may be functionally relevant. Among the 50 genes most highly expressed in biofilms relative to planktonic (suspension-grown) cells, we were able to recover insertion mutations in 25 genes. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16787 GPL15645

16 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) 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) 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) 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 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) 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) 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 form biofilm on the surface of indwelling medical devices. Biofilm formation is an importanat clinical problem because biofilm-grown cells have decreased susceptibility to antifungal agents. Microarray technology was used to identify changes in gene expression during biofilm development. Two biofilm substrates (denture and catheter) were used, with two C. albicans strains tested on each substrate. more...

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL5147

96 Samples

Download data: GPR

(Submitter supplied) Transcript profiling from 3 biological replicates of C. albicans strains expressing PGA22 under the control of a tetracycline derivative-inducible promoter grown during 16h in the presence or absence of 50 µg/mL doxycycline (Dox)

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL19289

3 Samples

Download data: GPR

(Submitter supplied) Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. We have combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (~10% of the genome) for genes affecting biofilm development in mixed-population experiments. The overexpression of 16 genes increased strain occupancy within a multi-strain biofilm, whereas overexpression of 4 genes decreased it. more...

Organism:

Candida albicans

Type:

Other

Platform:

GPL17420

8 Samples

Download data: GPR