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MetabolomicsGrowth control of the eukaryote cell: a systems biology study in yeast
Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each function...
2012-04-19 | MTBLS8 | MetaboLights
MetabolomicsEnergy-translation coupling limits yeast anaerobic growth

This study employs yeast as a model system to thoroughly investigate the differences in regulatory mechanisms under various nutrient limitation conditions, utilizing a systems biology approach integrated with techniques such as multi-omics analysis.To obtain a comprehensive quantitative landscap...

2026-05-24 | MTBLS14573 | MetaboLights
ProteomicsSWATH mass spectrometry performance using extended ion assay libraries
The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed using peptide MS/MS reference ion assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2016-05-12 | PXD002836 | Pride
Extended library Dia Swath 
MetabolomicsUntargeted lipidomics analysis of yeast metabolic proteins degradations to investigate the role of metabolic proteins in lipid metabolism
We combine auxin-inducible degradation of 500 characterized and 204 uncharacterized proteins with untargeted lipidomics providing a quantitative readout of cellular lipidomic states.
2026-03-24 | MTBLS14098 | MetaboLights
Genomicssequencing of yeast RNAi libraries for improved protein production
sequencing of yeast RNAi libraries for improved protein production
PRJEB27502 | ENA
TranscriptomicsGenome-wide Measurement of RNA Secondary Structure in Yeast
The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragme...
ORGANISM(S): Saccharomyces cerevisiae 
2010-08-24 | E-GEOD-22393 | biostudies-arrayexpress
ProteomicsBuilding high-quality assay libraries for targeted analysis of SWATH MS data
Targeted proteomics by selected/multiple reaction monitoring or, on a larger scale, by SWATH MS relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of critical importance. Here we present a detailed protocol that has been successfu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2015-01-26 | PXD001126 | Pride
Yeast Assay library Swath Spectral library 
TranscriptomicsRepertoire of miRNAs in epithelial ovarian cancer determined by next generation sequencing of small RNA cDNA libraries
Background: MicroRNAs (miRNAs) are small regulatory RNAs that are implicated in cancer pathogenesis and have recently shown promise as blood-based biomarkers for cancer detection. Epithelial ovarian cancer is a deadly disease for which improved outcomes could be achieved by successful early detectio...
ORGANISM(S): Homo sapiens 
2009-03-12 | E-GEOD-15190 | biostudies-arrayexpress
GenomicsOpen chromatin maps of genetically different yeast strains
Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enh...
ORGANISM(S): Saccharomyces cerevisiae 
2012-11-02 | E-GEOD-33466 | biostudies-arrayexpress
MetabolomicsMAVEN2: An Updated Open-Source Mass Spectrometry Exploration Platform

MAVEN, an open-source software program for analysis of LC-MS metabolomics data, was originally released in 2010. As mass spectrometry has advanced in the intervening years, MAVEN has been periodically updated to reflect this advancement. This manuscript describes a major update to the program, MA...

2024-07-22 | MTBLS3097 | MetaboLights
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