Yeast Colony Differentiation
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Michal Cap
PROVIDER: E-GEOD-35887 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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
Project description:MicroRNAs (miRNAs) are critical to proliferation, differentiation, and development. Here, we characterize gene expression in murine Dicer-null adult mesenchymal stem cell lines, a fibroblast cell type. Loss of Dicer leads to de-repression of let-7 targets at levels that exceed 10-100 fold with increases in transcription. Direct and indirect targets of this miRNA belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state. Surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 and the induction of let-7, upon differentiation, at embryonic day 10.5. Within this mid-gestation program, we characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss. In total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor suppressive function. Examination of genes directly bound by Flag-HA-NR6A1 in Dicer WT (Dicer f/f) adult mesenchymal stem cells (immortalized monoclonal lines of murine MSCs).
2013-04-10 | E-GEOD-44160 | biostudies-arrayexpress
Project description:LV fibroblasts were isolated from control (day 0), and infarcted regions at day 1, day 3, and day 7 after myocardial infarction (MI). Cells were isolated in DMEM in 10% fetal bovine serum and were seeded into 6-well plates and were allowed to grow to 80% confluence in DMEM supplemented with 10% fetal bovine serum (FBS). Cells were serum starved (DMEM + 0.1% FBS) for 18 h and then media was changed and secretome was collected after 24 h. The sample sizes are n=3 biological replicates for each time point.
2019-10-25 | PXD011778 | Pride
Project description:Macrophage secretome- Macrophages were isolated from the left ventricle from control (day 0) or from the infarct region at day 1 after myocardial infarction (MI). Cells were isolated in RPMI media with 0.1% fetal bovine serum and incubated for 2 hours and then spun at 800g for 5 min to separate cell debris. The sample sizes are n=4 biological replicates for each time point.
2022-05-19 | PXD011780 | Pride
Project description:While growing in the human intestine, C. jejuni grows within the mucus layer. The largest constituents of this layer are the large mucin glycoproteins. A transcriptomic profile of C. jejuni NCTC11168 growing in a mucin-containing minimal medium seeks to describe the effect of the presence of mucin proteins on the transcriptome of C. jejuni. Microarray data was collected from three independent biological replicates and 9 technical replicates for each biological replicate.
2011-04-01 | E-GEOD-28295 | biostudies-arrayexpress
Project description:Lef1 is a critical transducer of the Wnt/beta-catenin signaling pathway that is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag-tagged Lef1 in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Lef1 to understand how it regulates mesoderm differentiation and to establish the Lef1-regulated, Wnt/beta-catenin transcriptome. Total RNA was extracted from ES cells after 3 days of differentiating following Lef1 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes in untreated and doxycycline treated ES cells to identify Lef1 regulated genes.
2016-04-01 | E-GEOD-73083 | biostudies-arrayexpress
Project description:Sp5 is a target and critical transducer of the Wnt/beta-catenin signaling pathway and is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag epitope-tagged Sp5 protein in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Sp5 to understand how it regulates mesoderm differentiation by identifying important target genes which may mediate its activity. Total RNA was extracted from ES cells after 3 days of differentiating following F-Sp5 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes between untreated (minus) and doxycycline treated (plus) ES cells to identify Sp5 regulated genes.
2016-04-01 | E-GEOD-73082 | biostudies-arrayexpress
Project description:3 healthy cells - 3 DMD cells - 7 time points (tissue-derived myoblasts, tissue-derived myotubes, hiPSCs, Day 3 of differentiation, Day 10 of differentiation, Day 17 of differentiation, Day 25 of differentiation) - 1 replicate per cell line for the tissue-derived samples and 3 biological replicates per cell line for the hiPSC-derived samples.
2020-10-05 | E-MTAB-8321 | biostudies-arrayexpress
Project description:We employed RNA-seq to transcriptionally profile a pure population of hand-dissected polyploid TGCs from embryonic day 9.5. These data provide a set of polyploid-specific TGCs transcripts that will aid in the understanding of TGCs differentiation and endoreplication. TGCs were micro-dissected from day E9.5 nine implantation sites from C57BL/6J mice. The portion of the TGCs in direct contact with the spongiotrophoblast layer and the labyrinth layer were manually removed to avoid collecting any polyploid cells from the former or multi-nucleated syncytiotrophoblast cells from the latter.
2013-04-30 | E-GEOD-45782 | biostudies-arrayexpress
Project description:Streptococcus agalactiae (Group B Streptococcus, GBS) is a leading cause of early-onset neonatal bacterial infection. Evasion of innate immune defenses is critical to neonatal GBS disease pathogenesis. Effectors of the innate immune system such as antimicrobial peptides, as well as numerous antibiotics, target the peptidoglycan layer of the gram positive bacterial cell wall. The intramembrane-sensing histidine kinase class of two-component regulatory systems has recently been identified as important to the gram-positive response to cell wall stress. We identified and characterized the GBS homolog of LiaR, the response regulator component of the LiaFSR system and constructed site-directed, non-polar deletion mutations in the regulator gene liaR. GBS LiaR deletion mutant strains are more susceptible to cell wall active antibiotics (vancomycin and bacitracin) as well as antimicrobial peptides (colistin, nisin and the human cathelicidin LL-37) compared to isogenic wild-type GBS. LiaR mutant GBS are significantly attenuated in mouse models of both GBS sepsis and GBS pneumonia. To determine the genes regulated by LiaR that account for these defects, transcriptional profiling was performed using DNA microarray analysis, comparing wild-type GBS to LiaR mutant GBS under non-stressed conditions. Two separate RNA samples were extracted for each condition. One flip-dye replicate (2 hybridizations) was obtained for each pair of RNA samples for 4 hybridizations total.
2012-11-18 | E-GEOD-14571 | biostudies-arrayexpress