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GSE55508
Saccharomyces cerevisiae
12 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast grown in synthetic complete medium (SD) until glucose depletion is aged chronologically. Cells are stressed by lacking of nutrients and accumulating toxic substances, and thus undergo gene expression changes in response to those.
Publication Title
Genome-wide expression analyses of the stationary phase model of ageing in yeast.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The protein secretory pathway must maintain homoeostasis while producing a wide assortment of proteins in different conditions. It is also used extensively to produce many useful proteins in biotechnology. As such, secretory pathway dysfunction can be highly detrimental to the cell, resulting in the molecular basis for many human diseases, and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging.
Publication Title
Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
In this study we focus on two Saccharomyces cerevisiae strains with varying production of heterologous -amylase and we compare the metabolic fluxes and transcriptional regulation at aerobic and anaerobic conditions, in particular with the objective to identify the final electron acceptor for protein folding.
Publication Title
Anaerobic α-amylase production and secretion with fumarate as the final electron acceptor in Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
In this study we focus on two Saccharomyces cerevisiae (CEN. PK series) strains producing either insulin precursor or amylase and we compare the transcriptional regulation at different dilution rates, in particular with the objective to identify the relationship between cell metabolism and recombinant protein production.
Publication Title
Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae.
Sample Metadata Fields
Treatment
View Samples- Saccharomyces cerevisiae
- 24 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Alzheimers disease (AD) is a progressive neurodegenerative disorder. Oligomers of Amyloid- peptides (A) are thought to play a pivotal role in AD pathogenesis, yet the mechanisms involved remain unclear. Two major isoforms of A associated with AD are A40 and A42, the latter being more prone to form oligomers and toxic. Humanized yeast models are currently applied to unravel the cellular mechanisms behind A toxicity. Here, we took a systems biology approach to study two yeast AD models which expressed either A40 or A42 in bioreactor cultures. Strict control of oxygen availability and culture pH, strongly affected the chronological lifespan and reduced confounding effects of variations during cell growth. Reduced growth rates and biomass yields were observed upon expression of A42, indicating a redirection of energy from growth to maintenance. Quantitative physiology analyses furthermore revealed reduced mitochondrial functionality and ATP generation in A42 expressing cells, which matched with observed aberrant fragmented mitochondrial structures. Genome-wide expression levels analysis showed that A42 expression triggers strong ER stress and unfolded protein responses (UPR). Expression of A40 induced only mild ER stress, leading to activation of UPR target genes that cope with misfolded proteins, which resulted in hardly affected physiology. The combination of well-controlled cultures and AD yeast models strengthen our understanding of how cells translate different levels of A toxicity signals into particular cell fate programs, and further enhance their role as a discovery platform to identify potential therapies.
Publication Title
Interplay of Energetics and ER Stress Exacerbates Alzheimer's Amyloid-β (Aβ) Toxicity in Yeast.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
In the yeast Saccharomyces cerevisiae, accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates the unfolded protein response (UPR) mediated by Hac1p, whereas the heat shock response (HSR) mediated by Hsf1p mainly regulates cytosolic processes and protects the cell from different stresses. In this study, we find that a constitutive activation of the HSR by over-expression of a mutant HSF1 gene could relieve ER stress in both wild type and hac1 UPR-deficient cells.
Publication Title
Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 9 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
To study how the presence of PUFAs influences central cellular processes, and in order to perform lipidome, transcriptome and molecular studies we decided to use yeast as a model organism. We therefore co-expressed 12-desaturase and 6- desaturase genes from Mucor rouxii in S. cerevisiae with the objective to obtain a yeast strain that contains PUFAs, especially linoleic acid (LA, C18:29,12) and -linolenic acid (GLA, C18:36,9,12), in its membranes.
Publication Title
Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress.
Sample Metadata Fields
Time
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We undertook an inter-laboratory effort to generate high-quality quantitative data for a very large number of cellular components in yeast using transcriptome and metabolome analysis. We ensured the high-quality of the experimental data by evaluating a wide range of sampling and measurement techniques. The data were generated for two different yeast strains, each growing under two different growth conditions and based on integrated analysis of the high-throughput data we hypothesize that differences in growth rates and yields on glucose between the two strains are due to differences in protein metabolism.
Publication Title
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 1 Downloadable Sample
Illumina HiSeq 2000
Description
Overall goal: To identify genes that will cause non-fusogenic fibroblasts to become fusogenic. Purpose of analysis: To generate transcriptional profile of non-fusogenic fibroblasts, using 10T1/2 fibroblasts transduced with empty retrovirus as model. Experimental structure: The profile generated from the RNAseq analysis would be compared with transcriptional profile of MyoD-expressing fibroblasts (GEO DataSet GSE34907) to identify genes regulating fusion in muscle cells. Overall design: RNAseq analysis of total RNA from 10T1/2 fibroblasts transduced with retrovirus carrying empty pBabe-X retroviral vector was carried out to generate a transcriptional profile of a model of non-fusogenic fibroblasts.
Publication Title
Myomerger induces fusion of non-fusogenic cells and is required for skeletal muscle development.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 4000
Description
Blood-retina barrier (BRB) formation and retinal angiogenesis depend on beta-catenin signaling induced by the ligand norrin (NDP), the receptor frizzled4 (FZD4), co-receptor LRP5, and the tetraspanin TSPAN12. Impaired NDP/FZD4 signaling causes familial exudative vitreoretinopathy (FEVR), which may lead to blindness. Endothelial-cell specific inactivation of the Tspan12 gene at P28 using a Cdh5-CreERT2 driver shows that TSPAN12 functions in ECs to promote vascular morphogenesis and BRB formation in developing mice, and BRB maintenance in adult mice. 12 month after Tspan12 inactivation and loss of BRB maintenance with massive IgG and albumin extravasation we observe complement activation, cystoid edema, and impaired beta-wave in electroretinograms. RNA-Seq 6 month after Tspan12 inactivation provides a detailed view on the transcriptional response, including activation of antibody effector systems (complement and Fc receptors), inflammation and microglia responses, extracellular matrix organization and remodeling, and other responses. Overall design: Endothelial cell-specific inactivation of floxed Tspan12 was induced at P28 using a Cdh5-CreERT2 driver and total retina RNA (ribodepleted) from 4 control or ECKO retinas (8 samples) was subjected to RNA-Seq 6 months later
Publication Title
Endothelial Cell-Specific Inactivation of TSPAN12 (Tetraspanin 12) Reveals Pathological Consequences of Barrier Defects in an Otherwise Intact Vasculature.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples