Yeast cell cycle
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE4987 | GEO | 2006/08/05
SECONDARY ACCESSION(S): PRJNA95491
REPOSITORIES: GEO
Similar Datasets
Project description:Transcription profiles across the cell cycle of yox1 deleted yeast cells. BY2399 cells (yox1 delete cells isogenic with W303a) were arrested with alpha factor in YEPD media. After release from arrest cells were sampled every 5 min for 2 hr. Keywords: cell cycle time course
2007-09-30 | GSE5376 | GEO
Project description:Transcription profiles across the cell cycle of yox1 deleted yeast cells. BY2399 cells (yox1 delete cells isogenic with W303a) were arrested with alpha factor in YEPD media. After release from arrest cells were sampled every 5 min for 2 hr. Keywords: cell cycle time course Cells were synchronized with alpha factor and sampled every 5 min across 2 cell cycles. A total of 25 samples were analyzed. Technical replicates were included. cDNA of the cell cycle samples were labelled with Cy5. For Cy3 labelling, asynchronous yeast population was used.
2007-09-29 | E-GEOD-5376 | biostudies-arrayexpress
Project description:SSD1 is a polymorphic locus in budding yeast with many pleiotropic effects. Our lab had previously done transcript microarray of W303a in an ssd1-d background, and here we have carried out another transcript microarray across the cell cycle in an isogenic SSD1-V background. We find that a large fraction of budding yeast transcripts is differentially expressed in these cells. Ssd1 has recently been shown to bind mRNAs in vivo, but very few of these mRNAs show significant changes in levels in the SSD1-V versus ssd1-d comparison. About 20% of cell cycle-regulated transcripts are affected by SSD1-V and most of these transcripts show sharper amplitudes of oscillation in SSD1-V cells. Many transcripts whose gene products influence longevity are also affected, the largest class of which are involved in translation. Ribosomal protein mRNAs are globally down-regulated by SSD1-V. Cells were synchronized with alpha factor and sampled every 10 min across 2 cell cycles. A total of 13 samples were analyzed. No replicates were included. cDNA of the cell cycle samples were labelled with Cy5. For Cy3 labelling, asynchronous yeast population was used.
2010-05-06 | E-GEOD-16911 | biostudies-arrayexpress
Project description:SSD1 is a polymorphic locus in budding yeast with many pleiotropic effects. Our lab had previously done transcript microarray of W303a in an ssd1-d background, and here we have carried out another transcript microarray across the cell cycle in an isogenic SSD1-V background. We find that a large fraction of budding yeast transcripts is differentially expressed in these cells. Ssd1 has recently been shown to bind mRNAs in vivo, but very few of these mRNAs show significant changes in levels in the SSD1-V versus ssd1-d comparison. About 20% of cell cycle-regulated transcripts are affected by SSD1-V and most of these transcripts show sharper amplitudes of oscillation in SSD1-V cells. Many transcripts whose gene products influence longevity are also affected, the largest class of which are involved in translation. Ribosomal protein mRNAs are globally down-regulated by SSD1-V.
2009-09-01 | GSE16911 | GEO
Project description:The photosynthetic model marine diatom Phaeodactylum tricornutum was cultured with varying nitrogen sources and availability to elicit shifts in the proteome. Cells were grown to mid-exponential phase on ammonium (880 uM), collected by centrifugation and resuspended in N-free media for 2 hrs, and spiked with nitrate (150 uM) for 90 min. Cells were again collected by centrifugation, washed in N-free media, and resuspended in experimental treatments with no nitrogen (N-) and a nitrogen source (300 uM) provided as ammonium, nitrite, or nitrate. Each experimental treatment was sampled after 15 min, 45 min, and 18 hr.
2019-09-25 | PXD015061 | Pride
Project description:Nucleosome organization determines local chromatin structure and changes in nucleosome occupancy during the cell cycle are correlated with nuclear functions. We used oligonucleotide tiling arrays to analyze the cell cycle dependence of nucleosome occupancy at cohesin binding sites in yeast chromosomes. Processed data included in Series table. Data processing: To improve the signal to noise ratio, the raw data were first processed with dCHIP with its PM/MM difference model and invariant set normalization method, using the entire dataset. 8251 out of the total 92812 probe pairs were excluded from further analysis because they either have multiple hits in the genome or the signal from the genomic hybridization was too weak (cutoff at (PM-MM)/MM < 0.25). After Gaussian smoothing (s =75 bp), the data were normalized by that of the genomic DNA. These values were then converted to log2 scale. The mean was then computed for each array. To facilitate comparisons, the different datasets were rescaled to have the same mean with log2 value of 0. The log2 ratio along the four chromosomes at all the cell cycle stages are included. The ID represents "Chromosome No_chromosomal coordinate". Keywords: time course Yeast cells were arrested at G1/S boundary with alpha factor, then released for 15 min, 40 min, 65 min and 95 min respectively. Cells were collected at each time points, then mononucleosomal DNA was purified and hybridized to Affymetrix oligonucleotide tiling arrays. Total genomic DNA was hybridized as normalization signal.
2010-05-26 | E-GEOD-8130 | biostudies-arrayexpress
Project description:The photosynthetic model marine diatom Phaeodactylum tricornutum was cultured under conditions varying nitrogen content and availability, or varying iron concentrations over diel cycles to elicit shifts in the proteome and phosphoproteome. For the nitrogen experiments, cells were grown to mid-exponential phase on ammonium (880 uM), collected by centrifugation and resuspended in N-free media for 2 hrs, and spiked with nitrate (150 uM) for 90 min. Cells were again collected by centrifugation, washed in N-free media, and resuspended in experimental treatments with no nitrogen (N-) and a nitrogen source (300 uM) provided as ammonium, nitrite, or nitrate. Each experimental treatment was sampled after 15 min, 45 min, and 18 hr. For iron experiments, steady-state axenic cultures were maintained under a diel cycle of 12h light: 12h darkness and at three different concentrations of Fe' (Fe' is the sum of all Fe species not complexed to EDTA): a low concentration (20 pM Fe'), intermediate concentration (40 pM Fe') and at Fe-replete levels (400 pM Fe'). Samples were taken every four hours.
2020-04-17 | PXD015059 | Pride
Project description:Transcript profiling from a population of cell-cycle-arrested B-type cyclin mutant budding yeast. We compared transcript to protein expression levels in mutant cells.
2018-10-10 | GSE104904 | GEO
Project description:Gene expression data for cdc28-13 yeast released synchronously into the cell cycle. cdc28-13 yeast were arrested in G1 for 3 hours at 37 degrees. Cells were rapidly cooled to 25 C by mixing with an equal volume of media at 13 C, and time points were taken every 10 minutes. Cells were rapidly pelleted, and mRNA was isolated and hybridized against midlog mRNA.
2015-05-01 | E-GEOD-13232 | biostudies-arrayexpress
Project description:Yeast strain BY4741 was grown overnight at 30C in YPD rich media. The yeast culture was diluted to an OD600 of 0.1 using fresh YPD media and further grown until an OD600 of 0.2. Then, alpha -factor mating pheromone (GenScript) was added to a final concentration of 10 uM to allow cell synchronization at G1 phase. After 2.5 h, the alpha-factor was removed by harvesting the cells for 10 min at 6000 rpm and decanting supernatant. The arrested cells were inoculated in fresh YPD rich medium to be released from G1-arrest. Samples were collected at 0, 30, 40, 50, and 70 mins, 7.5 ml samples were collected for RNA extraction while 40 ml samples were taken for nucleosomal DNA preparation and for flow cytometry (FACS). Samples for RNA isolation were collected by pipetting the culture directly into 15-ml Falcon tubes containing 7.5 ml of icy-water to quickly chill the cells. Cells were harvested by spinning for 3-4 min at 6000 rpm, frozen in liquid N2 and stored at - 80C. Total cellular RNA was extracted using the RNeasy kit (Qiagen), following the manufacturerM-^Rs instructions with the spheroplasting protocol. Purified RNA samples were quantified by Qubit fluorometer (Invitrogen, Inc.) and Nanodrop spectrophotometer (Thermo Scientific, Inc.). The total RNA was hybridized to Affymetrix GeneChip Yeast Genome 2.0 arrays for gene expression analysis.
2012-09-01 | E-MEXP-3702 | biostudies-arrayexpress