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MetabolomicsLiquid chromatography coupled to high-resolution mass spectrometry metabolomics: A useful tool for investigating tumor secretome based on a three-dimensional co-culture model

Three-dimensional (3D) cell culture technologies, which more closely mimic the complex microenvironment of tissue, are being increasingly evaluated as a tool for the preclinical screening of clinically promising new molecules, and studying of tissue metabolism. Studies of metabolites released int...

2023-12-12 | MTBLS5375 | MetaboLights
MetabolomicsMetabolomics guides rational development of a simplified cell culture medium for drug screening against Trypanosoma brucei
In vitro culture methods underpin many experimental approaches to biology and drug discovery. The modification of established cell culture methods to be more biologically relevant, or to optimise growth, is traditionally a laborious task. Emerging metabolomics technology enables rapid evaluation of ...
2015-05-14 | MTBLS49 | MetaboLights
ProteomicsTime-Resolved Analysis of the Cell Wall Proteome in Saccharomyces cerevisiae S288c During Batch Fermentation
In this study, we aimed to characterize the temporal remodeling of the yeast cell wall proteome during the progression of a batch culture in a bioreactor using a rich medium. The model organism used was Saccharomyces cerevisiae strain S288c, cultivated in rich medium. Cell samples were collected at ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2026-09-07 | PXD071725 | Pride
Proteomics Yeast Bioreactor Cell wall Batch culture Kinetics Lc-ms/ms 
TranscriptomicsNutritional homeostasis in batch and steady-state culture of yeast.
This data file contains all the data used to produce Figure 4 of Saldanha, Brauer and Bostein. The limiting nutrient is indicated by the letter followed by the timecourse number. S= sulfate, P=phosphate, U=uracil, L=leucine. The chemostat comparisons are prefixed by CC. Channels are as noted in the ...
ORGANISM(S): Saccharomyces cerevisiae 
2005-07-16 | E-GEOD-2953 | biostudies-arrayexpress
TranscriptomicsMetabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
Bacteria in the genus Streptomyces are soil dwelling oligotrophs and important producers of secondary metabolites. Previously we showed that global mRNA expression was subject to a series of metabolic and regulatory switches during the life time of a fermentor batch culture of S. coelicolor M145. He...
ORGANISM(S): Streptomyces coelicolor 
2011-12-31 | E-GEOD-31068 | biostudies-arrayexpress
TranscriptomicsTranscriptomic reprogramming of Ethanol adapted vs Ethanol non adapted culture
We have previously shown that fed-batch processes with the longest uncoupling phase (ethanol adapted) were characterized by induction of storage carbohydrates, a metabolic event typical of yeast cells experiencing nutrient limitation, at the onset of this phase, whereas this metabolic event was not ...
ORGANISM(S): Saccharomyces cerevisiae 
2009-08-31 | E-GEOD-15321 | biostudies-arrayexpress
ProteomicsDDA-PASEF and diaPASEF acquired HCC1806/HS578T proteomic datasets with deliberate batch effects
We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: HCC1806 vs HS578T), a...
ORGANISM(S): Homo sapiens (Human) 
2023-11-21 | PXD041391 | Pride
Dda Pasef Dia Hcc1806 Hs578t Batch effects 
TranscriptomicsTranscription analysis of E. coli processed at persistent and decreasing glucose limitation in a fed-batch cultivation
A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along...
ORGANISM(S): Escherichia coli W3110 
2010-05-19 | E-GEOD-10307 | biostudies-arrayexpress
ProteomicsDDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects
We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: A549 vs K562), allowi...
ORGANISM(S): Homo sapiens (Human) 
2023-11-21 | PXD041421 | Pride
Dda Pasef Dia K562 A549 Batch effects 
ProteomicsHyperosmolality in CHO Culture: Effects on Proteome
Chinese hamster ovary cells (CHO) were exposed to highly concentrated feed solution during a fed-batch cultivation which causes an unphysiological osmolality increase (>300 mOsm/kg) affecting cell physiology, morphology and proteome. To get a deeper insight into underlying molecular mechanisms invol...
ORGANISM(S): Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus) 
2022-05-20 | PXD027443 | Pride
Nlc-ms lfq proteomics Fed-batch Q exactive plus Cho Hyperosmolality Cell size 
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