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Saccharomyces cerevisiae
24 Downloadable Samples
Illumina HiSeq 2000
Description
The behavior of yeast cells during industrial processes such as the production of beer, wine and bioethanol has been extensively studied. By contrast, our knowledge about yeast physiology during solid state processes, such as bread dough, cheese or cocoa fermentation remains limited. We investigated changes in the transcriptome of three genetically distinct Saccharomyces cerevisiae strains during bread dough fermentation. Our results show that regardless of the genetic background, all three strains exhibit similar changes in expression patterns. At the onset of fermentation, expression of glucose-regulated genes changes dramatically, and the osmotic stress response is activated. The middle fermentation phase is characterized by the induction of genes involved in amino acid metabolism. Finally, at the latest time point, cells suffer from nutrient depletion and activate pathways associated with starvation and stress response. Further analysis shows that genes regulated by the High Osmolarity Glycerol (HOG) pathway, the major pathway involved in the response to osmotic stress and glycerol homeostasis, are among the most differentially expressed genes at the onset of fermentation. More importantly, deletion of HOG1 and other genes of this pathway significantly reduces fermentation capacity. Together, our results demonstrate that cells embedded in a solid matrix such as bread dough suffer severe osmotic stress, and that a proper induction of the HOG pathway is critical for an optimal fermentation.
Publication Title
Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 23 Downloadable Samples
- NextSeq 500
Description
Comparison of genomic data from astrocytes and non-astrocyte cells from mice with or without FGF+EGF after SCI. We conducted genome-wide RNA sequencing of (i) immunoprecipitated astrocyte-specific ribosome-associated RNA (ramRNA) and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells, from spinal cord tissue of mice recieving i) SCI alone, ii) SCI+hydrogel depot containing FGF+EGF, or iii) SCI+empty hydrogel depot. Overall design: Young adult mGFAP-Cre-RiboTag mice underwent severe crush SCI at thoracic level 10. Hydrogel depots were injected two days post-injury. At 14 days following SCI, the central 3mm of the SCI lesion was extracted, homogenized and (i) astrocyte-specific ribosome-associated RNA (ramRNA) precipitated via a hemagglutinin (HA) tag targeted to astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples.
Publication Title
Required growth facilitators propel axon regeneration across complete spinal cord injury.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 32 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Clinical symptoms of dengue virus (DENV) infection, the most prevalent arthropod-borne viral disease, range from classical mild dengue fever to severe, life-threatening dengue shock syndrome. However, most DENV infections cause few or no symptoms. Asymptomatic DENV-infected patients provide a unique opportunity to decipher the host immune responses leading to virus elimination without negative impact on an individuals health. We used an integrated approach of transcriptional profiling and immunological analysis to compare a Cambodian population of strictly asymptomatic viremic individuals with clinical dengue patients. Whereas inflammatory pathways and innate immune response pathways were similar between asymptomatic individuals and clinical dengue patients, expression of proteins related to antigen presentation and subsequent T and B cell activation pathways were differentially regulated, independent of viral load and previous DENV infection history. Feedback mechanisms controlled the immune response in asymptomatic viremic individuals, as demonstrated by increased activation of T cell apoptosis-related pathways and FcRIIB signaling associated with decreased anti-DENV specific antibody concentrations. Taken together, our data illustrate that symptom-free DENV infection in children is associated with determined by increased activation of the adaptive immune compartment and proper control mechanisms, leading to elimination of viral infection without excessive immune activation, with implications for novel vaccine development strategies
Publication Title
Increased adaptive immune responses and proper feedback regulation protect against clinical dengue.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 17 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
This experiment was performed to identify immediate early genes that were induced by PDGF specifically through Src family kinases (SFKs), MEK1/2, or PI 3-K.
Publication Title
Platelet-derived growth factor stimulates Src-dependent mRNA stabilization of specific early genes in fibroblasts.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 364 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Cellular and tissue defects associated with insulin resistance are coincident with transcriptional abnormalities and are improved after insulin sensitization with thiazolidinedione (TZD) PPAR ligands.
Publication Title
Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization.
Sample Metadata Fields
Specimen part, Subject
View Samples
GSE4725- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Systemic arterial smooth muscle cells are exposed to a broad range of oxygen concentrations under physiological conditions. Hypoxia can modulate the proliferative response of smooth muscle cells leading to speculation about its role in vasculogenesis, vascular remodelling and the pathogenesis of arterial disease. The effect of hypoxia has been inconsistent, however, with both enhanced proliferation and growth arrest reported. Nevertheless, these reports support an important effect of hypoxia on smooth muscle cell proliferation and, given its physiological and clinical relevance, this requires clarification. We posited that variation in O2 concentration, within the range that exists in vivo, may have different effects on the proliferation and survival of vascular smooth muscle cells.
Publication Title
Oxygen regulation of arterial smooth muscle cell proliferation and survival.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Comparative analysis of FACS-sorted CCR2- and CCR2+ HSC in the steady state. CCR2+ HSC have fourfold higher proliferative rates than CCR2- HSC, are are biased towards the myeloid lineage and dominate the migratory HSC population.
Publication Title
Myocardial Infarction Activates CCR2(+) Hematopoietic Stem and Progenitor Cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina HiSeq 2500
Description
RNAseq (3''DGE) profiles of osteoblasts from four lung cancer-bearing mice and three tumor-free mice. Overall design: Osteoblasts were FACS-sorted using the following markers: CD45-CD31-Terr119-GFP+ from lineage depleted bone and bone marrow tissue of lung tumor-bearing or tumor-free age-, sex- and litter-matched KrasLSL-G12D/WT;p53Flox/Flox (KP)-Ocn GFP mice. Total RNA was prepared using the Trizol method followed cDNA preparation, amplification, Illumina adapter ligation and 3''end sequencing by Illumina HiSeq 2500
Publication Title
Osteoblasts remotely supply lung tumors with cancer-promoting SiglecF<sup>high</sup> neutrophils.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Interferon (IFN) is a unique type I IFN that is not induced by pattern-recognition response elements. IFN is constitutively expressed in mucosal tissues including the female genital mucosa. We show here that IFN induces an antiviral state in human macrophages that blocks HIV-1 replication.
Publication Title
IFN-<b>ε</b> protects primary macrophages against HIV infection.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Escherichia coli
- 8 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression.
Publication Title
A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.
Sample Metadata Fields
No sample metadata fields
View Samples