Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA94431 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, the transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper, since supplementation of 80 µM CuSO4 in YPD media could increase carotenoid yield 9.2-fold
2021-01-05 | GSE164229 | GEO
Project description:We used RNA-Seq to measure transcript abundance in 15 Saccharomyces cerevisiae strains from a diverse range of genetic lineages when growing in rich media (YPD) to characterize differential expression across strains.
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Project description:Extensive transcriptional heterogeneity revealed by isoform profiling Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5' capped mRNA transcription start site and the 3' polyadenylation site in different conditions: WT cells grown in glucose media [ypd, 2 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)], WT cells grown in galactose media [ypgal, 4 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)]. A modified protocol designed to enrich in long mRNA molecules was performed for WT cells grown in glucose media [ypd, 2 biological replicates (bio)] and in galactose media [ypgal, 2 biological replicates (bio)] conditions. Finally, control samples performed with a modified protocol designed to identify non-capped but polyadenylated molecules was performed in WT cells grown both in glucose (nypd) and galactose (nypgal) media.
2013-05-06 | E-GEOD-39128 | biostudies-arrayexpress
Project description:Gene expression in whi3 and WHI3x4 in YPD and YPE
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Project description:Dynamic mRNA gene expression following a rapamycin treatment
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Project description:Target of rapamycin complex 1 (TORC1) is implicated in growth control and aging from yeast to humans. Fission yeast is emerging as a popular model organism to study TOR signaling, although rapamycin has been thought to not affect cell growth in this organism. Here we analyzed the effects of rapamycin and caffeine, singly and combined, on multiple cellular processes in fission yeast. The two drugs led to diverse and specific phenotypes that depended on TORC1 signaling pathway inhibition, including prolonged chronological lifespan, inhibition of global translation, inhibition of cell growth and division, and reprogramming of global gene expression mimicking nitrogen starvation. Rapamycin and caffeine differentially affected these various TORC1-dependent processes. Combined drug treatment augmented most phenotypes and effectively blocked cell growth. Although rapamycin showed a much more subtle effect on global translation than did caffeine, rapamycin was more effective in prolonging chronological lifespan. Rapamycin prolonged the lifespan of non-growing cells only when applied during the growth phase but not when applied after cells had stopped proliferation. The doses of rapamycin and caffeine strongly correlated with growth inhibition and with lifespan extension. This comprehensive analysis will inform future studies into TORC1 function and cellular aging in fission yeast and beyond.
2013-05-05 | E-MTAB-1489 | biostudies-arrayexpress
Project description:To understand the gene expression in Saccharomyces cerevisiae under fermentative and respiraotry conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of S. cerevisiae wild type, sef1 deletion, and hyperactive SEF1-VP16 mutants under the YPD and YPGly conditions.
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Project description:A caffeine-resistant Saccharomyces cerevisiae mutant strain was obtained using an evolutionary engineering strategy based on successive batch cultivation at gradually increasing caffeine levels. The mutant strain Caf905-2 was selected at a caffeine concentration where its reference strain could not grow at all. Whole-genome transcriptomic analysis of Caf905-2 was performed with respect to its reference strain.
2018-12-28 | GSE124452 | GEO
Project description:To comparatively analyze the transcriptional responses of yeast cells to the presence of rapamycin or caffeine the homozygous hoΔ/hoΔ strain of S. cerevisiae BY4743 were grown in fully controlled fermenters in the presence of 200 nM rapamycin or 5 mM caffeine. Cells were cultured overnight in YPD medium (2% [w/v] D-glucose, 2% [w/v] peptone, 1% [w/v] yeast extract) at 30°C in an orbital shaker at 180 rpm prior to the fermentations. For the cultivations in the fermenters defined synthetic medium was used. The batch cultivations were carried out in duplicates in 2L B-Braun Biostat B Plus fermenters with 1.5L working volume kept at 30°C with the rate of agitation at 800rpm. pH was controlled at 5.5 with 0.5M NaOH and HCl. Sampling was carried out at the mid-exponential phase of growth at an OD range of 0.6-0.8. Samples harvested for the transcriptome analysis were immediately frozen in liquid nitrogen and were stored at -80oC until RNA isolation.
2019-03-15 | E-MTAB-7373 | biostudies-arrayexpress
Project description:To characterize gene expression that is dependent on the strength of calorie restriction (CR), we obtained transcriptome at different levels of glucose, which is a major energy and carbon source for budding yeast. To faithfully mimic mammalian CR in yeast culture, we reconstituted and grew seeding yeast cells in fresh 2% YPD media before inoculating into 2%, 1%, 0.5% and 0.25% YPD media to reflect different CR strengths. We collected and characterized 160 genes that responded to CR strength based on the rigorous statistical analyses of multiple test corrected ANOVA (adjusted é value < 0.1 or raw é value < 0.0031) and Pearson correlation (|r| > 0.7). Based on the individual gene studies and the GO Term Finder analysis of 160 genes, we found that CR dosedependently and gradually increased mitochondrial function at the transcriptional level. Therefore, we suggest these 160 genes are markers that respond to CR strength and that might be useful in elucidating CR mechanisms, especially how stronger CR extends life span more. Experiment Overall Design: Different glucose levels: 2%, 1%, 0.5%, and 0.25% Experiment Overall Design: Three biological replicates in each level
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