GEO DataSets

(Submitter supplied) Wild yeast and many clinical strains form complex, biofilm colonies, providing protection from desiccation, drugs and other stresses. Few transcriptomic studies have focused on sub-surface invasive “roots” due to the challenges of cell isolation from agar and subpopulation cross-contamination. Here we present, a first transcriptomic analysis via RNA sequencing of root and aerial cells, separated by a novel method. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

6 Samples

Download data: TXT

(Submitter supplied) Transcriptome comparison of cells from 4 and 7 day-old microcolonies of wild Saccharomyces cerevisiae BR-F strain, 4 and 7 day-old microcolonies of feral BR-RF strain and 4- and 7 day-old microcolonies of domesticated BR-S strain. All colonies grown on solid complex media with glycerol as carbon source. The aim of the study was to identify genes required for fluffy (structured) colony formation as well as the genes specific for certain phenotypic variant. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3458

18 Samples

Download data: MEV

(Submitter supplied) When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

18 Samples

Download data: CEL

(Submitter supplied) Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance. Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast S. cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1 and ROF1/YHR177W as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and non-biofilm forming strains revealed that all of the overexpression strains, other than DIG1 and TOS8, were adopting a single differential expression profile, although induced to varying degrees. TOS8 adopted a separate profile, while the expression profile of DIG1 reflected the common pattern seen in most of the strains, plus substantial DIG1-specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a real transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and non-biofilm states.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

20 Samples

Download data: TXT

(Submitter supplied) Purpose:To dissect the mechanisms underlying altered gene expression in aneuploids, we measured transcript abundance in colonies of haploid yeast strain F45 and derived strains, including strains disomic for chromosomes XV and XVI, using RNA-seq. F45 colonies display complex “fluffy” morphologies, while the disomic colonies are smooth, resembling laboratory strains Methods: RNA-seq analysis was carried out on RNA isolated from fully developed S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19756 GPL13821

35 Samples

Download data: TXT

(Submitter supplied) Transcription profile of different layers from S.cerevisiae colonies in day 15 and day 20.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL15249

7 Samples

Download data: MEV

(Submitter supplied) In this study, using DNA microarray analysis, we compared the comprehensive expression profiles of two yeast trains, i.e, the previously obtained ethanol-adapted yeast strain and the parental strain as control (FY834), under the ethanol stress condition (YPD medium contained 10% ethanol). As a result, we identified certain genes and functional categories of the genes that are possible involved in growth under the ethanol stress condition.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7698

2 Samples

Download data: GPR

(Submitter supplied) Yeast S. cerevisiae microarrays from the SGDB (Ecole Normale Superieure, Paris, France). Yeast ORFs are deposited in duplicate (double genome). Probes are oligonucleotides (40mers) from the Yeast oligoset distributed by MWG Biotech. Keywords = yeast Keywords = transcriptome

Organism:

Saccharomyces cerevisiae

2 Series

5 Samples

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(Submitter supplied) The parent S. cerevisiae strain, BY4741, and specific gene deletions of the parent S.cerevisiae strain BY4741 were treated with 100uM NaAsO2 (AsIII) for 2h and compared to the untreated counterpart (yap1Δ vs. yap1Δ 2h 100uM AsIII, cad1Δ vs. cad1Δ 2h 100uMAsIII, rpn4Δ vs. rpn4Δ 2h 100uM AsIII, arr1Δ vs. arr1Δ 2h 100uM AsIII, parent vs. parent with 2h 100uM AsIII). The untreated specific deletion strain was also compared to the untreated parent strain in order to identify differential expression of genes due to the knockout alone. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL884 GPL1474

40 Samples

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(Submitter supplied) Time course analyses of gene expression in sok2 deleted vs wild type colonies during late developmental stages on plate. Keywords = ammonia Keywords = metabolism Keywords = yeast Keywords = stress Keywords = transcriptome Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL1271 GPL1265

5 Samples

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(Submitter supplied) The budding yeast, Saccharomyces cerevisiae, has emerged as an archetype of eukaryotic cell biology. Here we show that S. cerevisiae is also a model for the evolution of cooperative behavior by revisiting flocculation, a self-adherence phenotype lacking in most laboratory strains. Expression of the gene FLO1 in the laboratory strain S288C restores flocculation, an altered physiological state, reminiscent of bacterial biofilms. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

4 Samples

Download data: CEL

(Submitter supplied) We report the development and application of isogenic colony sequencing to profile heterogeneity among yeast colonies. We profiled transcriptomes of the opaque-white switching in C. albicans colonies and an ARO4 mutagenesis library in S. cerevisiae colonies.

Organism:

Saccharomyces cerevisiae; Candida albicans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23041 GPL17143

2 Samples

Download data: TXT