Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Abundances of transcripts, proteins, metabolites, and lipids in the cell cycle of budding yeast

ABSTRACT: cell cycle studies in the budding yeast Saccharomyces cerevisiae.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932)

SUBMITTER: Birgit Schilling

PROVIDER: MSV000084302 | MassIVE |

SECONDARY ACCESSION(S): PXD015345

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Abundances of transcripts, proteins metabolites and lipids in the cell cycle of budding yeast.

Project description:This entry contains the proteomic files from a data set of RNAs, proteins, metabolites and lipids analyzed from the same staged samples of S. cerevisiae cells across the cell cycle. Actively growing (un-arrested) diploid cells were collected by elutriation as 8 distinct size pools across the cell cycle in triplicate. Yeast in these 24 aliquots were lysed and soluble and insoluble proteins were prepared for shotgun LC-MS/MS mass spectrometry analysis.

2019-10-29 | PXD015273 | Pride

Abundances of transcripts, proteins, metabolites, and lipids in the cell cycle of budding yeast

Project description:Abundances of transcripts, proteins, metabolites, and lipids in the cell cycle of budding yeast

| PRJNA559005 | ENA

Abundances of transcripts, proteins, metabolites, and lipids in the cell cycle of budding yeast

Project description:For the first time in any system, we generated experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from un-arrested, growing, and synchronously dividing yeast cells.

2019-12-11 | GSE135476 | GEO

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

Project description:Cell-cycle transcript dynamics from two species of wild-type budding yeast growing at 30 degrees Celsius in rich media: Saccharomyces cerevisiae (BF264-15D background) and Cryptococcus neoformans var. grubii (H99F background). We compared programs of cell-cycle-regulated genes between distantly related budding yeasts.

2016-12-07 | GSE80474 | GEO

Small RNAs in budding yeast

Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and Y´ subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y´ mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.

2009-09-10 | GSE17871 | GEO

Small RNAs in budding yeast

Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and YM-BM-4 subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess YM-BM-4 mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi. Employ high-throughput sequencing of endogenous small RNAs from the budding yeasts Saccharomyces castellii, Kluyveromyces polysporus, Candida albicans, Saccharomyces cerevisiae, and Saccharomyces bayanus.

2009-09-10 | E-GEOD-17871 | biostudies-arrayexpress

Yeast FAIRE_Cell Cycle Study

Project description:The packaging of DNA into nucleosomes influences the accessibility of underlying regulatory information. Nucleosome occupancy and positioning are best characterized in the budding yeast Saccharomyces cerevisiae, albeit in asynchronous cell populations or on individual promoters such as PHO5 and GAL1–10. Using FAIRE (formaldehyde-assisted isolation of regulatory elements) and whole-genome microarrays, we examined changes in nucleosome occupancy throughout the mitotic cell cycle in synchronized populations of S. cerevisiae. Perhaps surprisingly, nucleosome occupancy did not exhibit large, global variation between cell cycle phases. However, nucleosome occupancy at the promoters of cell cycle–regulated genes was reduced specifically at the cell cycle phase in which that gene exhibited peak expression, with the notable exception of S-phase genes. We present data that establish FAIRE as a high-throughput method for assaying nucleosome occupancy. For the first time in any system, nucleosome occupancy was mapped genome-wide throughout the cell cycle. Fluctuation of nucleosome occupancy at promoters of most cell cycle–regulated genes provides independent evidence that periodic expression of these genes is controlled mainly at the level of transcription. The promoters of G2/M genes are distinguished from other cell cycle promoters by an unusually low baseline nucleosome occupancy throughout the cell cycle. This observation, coupled with the maintenance throughout the cell cycle of the stereotypic nucleosome occupancy states between coding and non-coding loci, suggests that the largest component of variation in nucleosome occupancy is “hard wired,” perhaps at the level of DNA sequence. Keywords: FAIRE

2006-08-11 | GSE4719 | GEO

Nucleosome Positioning Dynamics Through the Yeast Metabolic Cycle

Project description:We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression. Examination of nucleosome positions and transcriptional output through metabolic oscillations in budding yeast.

2016-03-15 | E-GEOD-77631 | biostudies-arrayexpress

Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae

Project description:Layers of regulation on cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae

| PRJNA414110 | ENA

RNA-seq of yeast cell cycle, used for absolute gene expression quantification

Project description:We use Saccharomyces cerevisiae to perform absolute quantitative multi-omics analysis to map interactions of different cellular processes during the yeast cell cycle.

2020-03-30 | E-MTAB-8565 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data