Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA94021 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A six array study using total gDNA recovered from two separate cultures of each of three different strains of Saccharomyces cerevisiae (YB-210 or CRB, Y389 or MUSH, and Y2209 or LEP) and two separate cultures of Saccharomyces cerevisiae DBY8268. Each array measures the hybridization of probes tiled across the Saccharomyces cerevisiae genome.
2014-10-01 | GSE56441 | GEO
Project description:This experiment aims to map nucleosome positions and comparison of the same in WT NORMAL GROWTH vs WT-NUTRIENT STARVATION/isw1∆2∆ MUTANT/rsc4-∆4 MUTANT in Saccharomyces cerevisiae using a custom designed tiling array on Agilent plat form. The corresponding platform is submitted to GEO under Geo-ID GPL15842. 60mer probes with variable tiling density were designed for all the genes transcribed by RNA polymerase III. Each gene is tiled along with its 1kb downstream and upstream region with the exceptions of RPR1, SCR1, RDN5(1-6) and SNR52. Mononucleosomal DNA and size matched naked DNA was competitively hybridized to the array. Data was extracted and normalized log ratios were calculated using Agilent sofware. Normalized log2 ratio data was used in MLM to detection nucleosome positions.
2013-06-21 | GSE39802 | GEO
Project description:We used ChIP-seq to determine the whole-genome enrichment of histone H3 threonine 11 phosphorylation (H3 T11ph) during Saccharomyces cerevisiae meiosis. S. cerevisiae SK1 cells were synchronized for meiotic entry and 3 and 4 hour meiotic samples were obtained. As H3 T11ph is dependent on the formation of meiotic double strand breaks (DSBs), a negative control ChIP-seq sample was obtained from a strain lacking DSBs (spo11-yf). Concurrently, ChIP-seq was carried out for histone H3 as a control for comparision.
2017-06-28 | GSE100564 | GEO
Project description:Background: Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse transcription in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions. Results: Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition specific anti-sense transcription levels is higher than that in condition specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse transcription in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse transcription, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes. Conclusions: This study provides a comprehensive picture of the role of antisense transcription mediating sense transcription in different conditions across yeast species. We can conclude from our findings that antisense regulation could act like an on-off switch on sense regulation in different conditions.
2014-06-09 | GSE58319 | GEO
Project description:<p>Despite extensive research on Saccharomyces cerevisiae functional genomics, approximately 880 out of ~6,000 open reading frames (ORFs) remain uncharacterised. In this study we propose a method for characterising genes with limited prior functional knowledge using an automated laboratory platform, in conjunction with several hypothesis instantiation methods. We demonstrate this method by investigating YGR067C, an uncharacterised ORF hypothesised to regulate respiration during the diauxic shift. Predictions of the first-order effects of deletion were obtained by curating a list of pathways relevant to the hypothesis. Higher-order effects were predicted using simulation models based on the GEM Yeast9. The predictions were tested using empirical data from biological experiments performed in the Robot Scientist Eve, which generated OD560, transcriptomics, and metabolomics data. </p><p>We observed that YGR067C deletion led to downregulation of transcripts in some ethanol consuming respiratory pathways during the glucose phase. During the ethanol phase we observed that NAD+, NADP+ and NADH accumulated, and several amino acid biosynthesis pathways were enriched for the ygr067c∆ strain, suggesting longer term consequences of YGR067C mediated regulation. Based on these observations we propose that the role of YGR067C during the diauxic shift is to regulate genes related to ethanol consumption and respiration in the glucose phase.</p>
2025-12-03 | MTBLS12663 | MetaboLights
Project description:Total RNA versus genomic DNA hybridization on custom arrays designed for all Saccharomyces cerevisiae genes
2010-07-06 | GSE22204 | GEO
Project description:Array CGH of interspecific hybrid yeasts using multi-species array platform
| PRJNA152665 | ENA
Project description:The polyploid S. cerevisiae karyotypes were analyzed by array-CGH to identify the deletion or duplication of gene or chromosome during the strain construction and after experimental evolution.
2016-10-11 | GSE76595 | GEO
Project description:LPS was used as a stressor to stimulate the model organism Saccharomyces cerevisiae. To detect extracellular metabolic information of VOCs. To provide a molecular basis for cellular metabolism of VOCs by proteome.
2023-12-18 | PXD047920 |
Project description:Proteomic analysis of the extracellular matrix of Saccharomyces cerevisiae W303-1A Wt and the isogenic mutant strain gup1Δ during the development of multicellular overlays.
2015-11-30 | PXD001133 | Pride