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Yeast Colony Differentiation

ABSTRACT: Transcription profile of different layers from S.cerevisiae colonies in day 15 and day 20.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE35887 | GEO | 2012/02/17

SECONDARY ACCESSION(S): PRJNA151943

REPOSITORIES: GEO

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Yeast Colony Differentiation

Project description:Transcription profile of different layers from S.cerevisiae colonies in day 15 and day 20. Lower layer (L-cells) vs upper layer (U-cells). 3 biological replicates for day 15 and two replicates for day 20 were used for the total of 4 and 3 technical replicates, respectively. Spotted oligonucleotide microarray slides contain double genome of S. cerevisiae. Dye-swap was performed in replicates

2012-02-17 | E-GEOD-35887 | biostudies-arrayexpress

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization

Project description:Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia.During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism and nitrate utilization were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and reveal how this fungus adapts as it colonizes complex environments.

2015-09-09 | PXD002130 | Pride

Expression profiling of various colony phenotypes of wild Saccharomyces cerevisiae strain

2014-02-19 | GSE40625 | GEO

Expression profiling of various colony phenotypes of wild Saccharomyces cerevisiae strain

Project description: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. BR-F is wild strain isolated from natural habitat and forms structured colonies when grown on media with non-fermentable carbon source. BR-S strain arose by phenotypic switch from the original wild BR-F strain during the cultivation of BR-F strain under rich and favourable conditions (process of so-called domestication), forms smooth colonies. BR-RF strain is derived from the domesticated BR-S strain under adverse conditions and restores the formation of structured colonies and other properties of original wild BR-F strain. Comparison of transcriptomes of cells from BR-F colonies vs cells from BR-RF colonies (see samples BR-FxBR-RF...), comparison of transcriptomes of cells from BR-F colonies vs cells from BR-S colonies (see samples BR-FxBR-S...) and comparison of transcriptomes of cells from BR-RF colonies vs cells from BR-S colonies (see samples BR-RFxBR-S...). Comparison of each couple performed with 4 day-old colonies and with 7 day-old colonies. 2 biological replicates for each time point from total 3 technical replicates (for first biological replicate see ...rep1, ...rep2 files, second biological replicate ...rep3 file). Dye-swap was performed between first two replicates (...rep1, ...rep2). In total six samples for each couple. Spotted ORFs microarray slides contain double genome of S. cerevisiae.

2014-02-19 | E-GEOD-40625 | biostudies-arrayexpress

Role of yeast Nup60 lysine 467 acetylation in regulation of transcription

Project description:Purpose: The experiment aimed to elucidate possible global effects of Nup60 K467 acetylation on transcription in S.cerevisiae. Result: Neither acetyl-mimic nor deacetyl-mimic mutations in Nup60K467 cause major shifts in expression profile.

2022-06-16 | GSE199740 | GEO

Bulk RNA sequencing of various morphological locations and colony differentiation stages of Cristatella mucedo

Project description:RNA-sequencing of Cristatella mucedo: two dissections of mature colonies, and characterization of different developmental stages starting from frozen statoblasts.

2019-12-11 | GSE141747 | GEO

Differential gene expression of cells located in the top and bottom of yeast colonies

Project description:Saccharomyces cerevisiae colonies were grown on synthetic minimal media containing 1% glucose. The top layer of cells was scraped off using a custom plastic guide and a cell scraper. The remaining bottom layer of cells was then washed off with water and proteomics samples were prepared from both layers separately. Label-free quantification by DIA-SWATH was used to assess differences in gene expression between top and bottom layers.

2023-02-13 | PXD033395 | Pride

High throughput gene expression profiling of yeast colonies with microgel-culture Drop-seq

Project description: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.

2019-04-17 | GSE121271 | GEO

Integrating Transcriptomic and ChIP-Seq Reveals Important Regulatory Regions Modulating Gene Expression in Myometrium during Implantation in Pigs [ChIP -seq]

Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the uterine circular muscle (CM) and longitudinal muscle (LM) layers at the mesometrial side on day 15 (implantation stage) of pregnancy, and the uterine CM layer at the mesometrial side on day 15 of the estrous cycle in pigs.

2023-01-25 | GSE216438 | GEO

Spatiotemporal trascriptomics of Bacillus subtilis swarming colony

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2023-09-20 | GSE224332 | GEO

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