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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of E.coli W3110 oxygen downshift

ABSTRACT: Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied. Experiment Overall Design: Four microarray chips were analyzed: Experiment Overall Design: S1 was taken 15 min before the oxygen downshift Experiment Overall Design: S2, S3 and S4 were taken 15 min, 45 min and 75 min after the oxygen downshift, respectively

ORGANISM(S): Escherichia coli

SUBMITTER: Jaakko Soini

PROVIDER: E-GEOD-12006 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Oxygen downshift experiment with E.coli W3110

Project description:Dynamical response to oxygen downshift under fermentation conditions was tested by taking sample before (S1) and after (S2, S3 and S4) the oxygen downshift. The dynamical changes relevant for ongoing research on physiology were applied.

2008-07-08 | GSE12006 | GEO

Transcription profiling of S. cerevisiae in carbon-limited anaerobic/aerobic growth

Project description:Addition of 3 new arrays made from carbon limited chemostat of CENPK113-7D and 3 new arrays made from aerobic carbon limited chemostat of CENPK113-7D Complmentary data to the data of the serie GSE1723. Experiment Overall Design: GSM108368, GSM 108369 and GSM108370 are biological replicates Experiment Overall Design: GSM108392, 108393, 108394 are biological replicates Experiment Overall Design: Complmentary data to the data of the serie GSE1723.

2008-06-13 | E-GEOD-4807 | biostudies-arrayexpress

Transcription profiling of mouse lung fibroblasts and Lewis lung cells to investigate the transciptional regulation that governs cell-cell fusion process

Project description:This study aimed to investigate the transciptional regulation that governs cell-cell fusion process.

2008-06-30 | E-TABM-381 | biostudies-arrayexpress

Transcription profiling of the response of Saccharomyces cerevisiae to desiccation and rehydration: Series 1

Project description:This series represents Experiment 1 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.

2007-10-23 | E-GEOD-1311 | biostudies-arrayexpress

Transcription profiling of the response of Saccharomyces cerevisiae to desiccation and rehydration: Series 3

Project description:This series represents Experiment 3 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.

2007-10-23 | E-GEOD-1313 | biostudies-arrayexpress

Transcription profiling of the response of Saccharomyces cerevisiae to desiccation and rehydration: Series 2

Project description:This series represents Experiment 2 of the yeast desiccation / rehydration time course analysis. Samples include Control, 50% dry, Dry, 15 min. post rehydration, 45 min. post rehydration, 90 min. post rehydration, and 360 min. post rehydration.

2007-10-23 | E-GEOD-1312 | biostudies-arrayexpress

Transcription profiling of S.pombe wild type and zfs1 deficient strains reveals zfs1 as an mRNA binding and destabilizing protein in Schizosaccharomyces pombe

Project description:Tristetraprolin is a vertebrate CCCH tandem zinc finger protein that can bind to and destabilize certain mRNAs containing AU-rich element binding sites. zfs1 is the single gene in the fission yeast, Schizosaccharomyces pombe, that encodes a protein containing the critical features of the tristetraprolin zinc finger domain. zfs1 has been linked to pheromone signal transduction control and to the coordination of mitosis, but no biological function has been ascribed to the zfs1 protein. Through a functional genomics approach we compared transcript levels in wild-type and zfs1-deficient S. pombe strains; those elevated in the zfs1-deficient strain were examined for the presence of potential tristetraprolin-like binding sites. One such potential target transcript was encoded by arz1, a gene encoding a protein of unknown function that contains armadillo repeats. arz1 mRNA decay was inhibited in the zfs1-deficient strain when it was expressed under the control of a thiamine-repressible promoter. Mutations within one AU-rich element present in the arz1 3prime-untranslated region protected this transcript from zfs1-promoted decay, whereas mutating another potential binding site had no effect. Binding assays confirmed a direct interaction between zfs1 and arz1 mRNA-based probes; this interaction was eliminated when key residues were mutated in either zfs1 zinc finger. zfs1 and its targets in S. pombe represent a useful model system for studies of zinc finger protein/AU-rich element interactions that result in mRNA decay. Experiment Overall Design: S. pombe wild-type and zfs1-deficient strains were grown to 1.0 A600 in EMM+5S at 30C for steady state analysis. Total cellular RNA was prepared from four replicate cultures.

2008-06-15 | E-GEOD-8122 | biostudies-arrayexpress

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

Project description:Deep proteomic analysis of mammalian cell lines would yield an inventory of the building blocks of the most commonly used systems in biological research. Mass spectrometry-based proteomics can identify and quantify proteins in a global and unbiased manner and can highlight the cellular processes that are altered between such systems. We analyzed 11 human cell lines using an LTQ-Orbitrap family mass spectrometer with a â€œhigh fieldâ€� Orbitrap mass analyzer with improved resolution and sequencing speed. We identified a total of 11,731 proteins, and on average 10,361 Â± 120 proteins in each cell line. This very high proteome coverage enabled analysis of a broad range of processes and functions. Despite the distinct origins of the cell lines, our quantitative results showed surprisingly high similarity in terms of expressed proteins. Nevertheless, this global similarity of the proteomes did not imply equal expression levels of individual proteins across the 11 cell lines, as we found significant differences in expression levels for an estimated two-third of them. The variability in cellular expression levels was similar for low and high abundance proteins, and even many of the most highly expressed proteins with household roles showed significant differences between cells. Metabolic pathways, which have high redundancy, exhibited variable expression, whereas basic cellular functions such as the basal transcription machinery varied much less. We harness knowledge of these cell line proteomes for the construction of a broad coverage â€œsuper-SILACâ€� quantification standard. Together with the accompanying paper (Schaab, C. MCP 2012, PMID: 22301388) (17) these data can be used to obtain reference expression profiles for proteins of interest both within and across cell line proteomes.

2024-04-25 | PXD051723 | Pride

Transcription profiling of S. cerevisiae treated with absence of oxygen or depletion of ATP to investigate control of glycolytic enzyme fluxes

Project description:Metabolic fluxes may be regulated "hierarchically," e.g., by changes of gene expression that adjust enzyme capacities (V(max)) and/or "metabolically" by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by transcription, translation, protein degradation, and posttranslational modification. The method was applied to the regulation of fluxes through individual glycolytic enzymes when the yeast Saccharomyces cerevisiae was confronted with the absence of oxygen and the presence of benzoic acid depleting its ATP. Metabolic regulation largely contributed to the approximately 10-fold change in flux through the glycolytic enzymes. This contribution varied from 50 to 80%, depending on the glycolytic step and the cultivation condition tested. Within the 50-20% hierarchical regulation of fluxes, transcription played a minor role, whereas regulation of protein synthesis or degradation was the most important. These also contributed to 75-100% of the regulation of protein levels. Experiment Overall Design: To quantify the regulation of the Vmax values and the fluxes at the different levels of gene expression, we measured how the fluxes through the glycolytic enzymes, the Vmax values, and the concentrations of these enzymes and their corresponding mRNA concentrations change when yeast is exposed to aerobic and anaerobic (with and without challenges.

2008-06-16 | E-GEOD-9232 | biostudies-arrayexpress

Identification of proteins crosslinked to lysosomal sphingosine and cholesterol probes

Project description:HeLa cells were labelled with lysosomally localized photocrosslinkable and clickable probes for sphingosine and cholesterol. Upon photocrosslinking and cell lysis, the protein-lipid complexes were clicked to biotin azide and enriched via Streptavidin-immunoprecipitation. Enriched protein-lipid complexes were then analyzed by LC-MS/MS to identify proteins interacting with sphingosine and cholesterol, respectively.

2023-02-07 | PXD039780 | Pride

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