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accession-icon SRP027561
Saccharomyces cerevisiae strain:Bread strain, Wine strain, Bioethanol strain Transcriptome or Gene expression
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina 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.

Alternate Accession IDs

None

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE6104
Rat right heart pulmonary embolism microarray
  • organism-icon Rattus norvegicus
  • sample-icon 45 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Time and dose related expression profiles of rat right heart tissue in microsphere bead model for Pulmonary embolism

Publication Title

Transcriptional profile of right ventricular tissue during acute pulmonary embolism in rats.

Alternate Accession IDs

E-GEOD-6104

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE19060
Analysis of Meniscal Degeneration and Meniscal Gene Expression
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Menisci play a vital role in load transmission, shock absorption and joint stability. The current dogma is that the menisci simply protects the cartilage and play no role in osteoarthritis (OA) unless they are injured. However, there is increasing evidence suggesting that OA menisci may not merely be bystanders in the disease process of OA. This study sought: 1) to determine the prevalence of meniscal degeneration in OA patients, 2) to examine gene expression in OA meniscal cells compared to normal control meniscal cells, and 3) to test the hypothesis that OA meniscal cells are different from normal meniscal cells.

Publication Title

Analysis of meniscal degeneration and meniscal gene expression.

Alternate Accession IDs

E-GEOD-19060

Sample Metadata Fields

Specimen part

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accession-icon GSE100935
Gene expression data of human gastric tumors
  • organism-icon Homo sapiens
  • sample-icon 61 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Tumors of advanced gastric cancer patients were biopsied and subjected to gene expression profiling using the Affymetrix Human Genome U133 Plus 2.0 Arrays. Patients were then segregated into G1, G2 or G3 groups based on their tumor genomic profiles. Patients in the G1 and G3 cohorts were assigned SOX (oxaliplatin plus S-1) chemotherapy whereas those in the G2 cohort were given SP (cisplatin plus S-1) regimen.

Publication Title

Real-Time Tumor Gene Expression Profiling to Direct Gastric Cancer Chemotherapy: Proof-of-Concept "3G" Trial.

Alternate Accession IDs

E-GEOD-100935

Sample Metadata Fields

Specimen part

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accession-icon GSE109403
Proteogenomic Analysis of Medulloblastoma
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.

Alternate Accession IDs

E-GEOD-109403

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE109401
Proteogenomic Analysis of Medulloblastoma [gene expression microarray]
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

These gene expression microarrays were performed as part of a project aiming to integrate quantitative proteomic, gene expression and epigenetic data from the childhood brain tumor medulloblastoma.

Publication Title

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential.

Alternate Accession IDs

E-GEOD-109401

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE26685
Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HumanWG-6 v3.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions.

Alternate Accession IDs

E-GEOD-26685

Sample Metadata Fields

Specimen part, Disease, Disease stage, Cell line, Treatment

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accession-icon GSE87557
Role of annexin A2 in muscle repair
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Repair of injured muscle involves repair of injured myofibers through the involvement of dysferlin and its interacting partners, including annexin. Studies with mice and patients have established that dysferlin deficit leads to chronic inflammation and adipogenic replacement of the diseased muscle. However, longitudinal analysis of annexin deficit on muscle pathology and function is lacking. Here we show that unlike annexin A1, but similar to dysferlin, lack of annexin A2 (AnxA2) causes poor myofiber repair and progressive weakening with age. However, unlike dysferlin-deficient muscle, AnxA2-deficient muscles do not exhibit chronic inflammation or adipogenic replacement. Deletion of AnxA2 in dysferlin deficient mice reduces inflammation, adipogenic replacement, and loss in muscle function caused by dysferlin deficit. These results show that: a) AnxA2 facilitates myofiber repair, b) chronic inflammation and adipogenic replacement of dysferlinopathic muscle requires AnxA2, and c) inhibiting AnxA2-mediated inflammation is a novel therapeutic avenue for dysferlinopathy.

Publication Title

Annexin A2 links poor myofiber repair with inflammation and adipogenic replacement of the injured muscle.

Alternate Accession IDs

E-GEOD-87557

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE26684
Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange [expression]
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HumanWG-6 v3.0 expression beadchip

Description

Genome wide gene expression profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The sample treated with non target siRNA and PBS serves as control sample.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-26684

Sample Metadata Fields

Specimen part, Disease, Disease stage, Cell line

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accession-icon GSE64574
Effect of MK591 on gene expression in LNCaP cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Cells were treated with MK591 and gene expression was analyzed with Illumina bead chip array.

Publication Title

No associated publication

Alternate Accession IDs

E-GEOD-64574

Sample Metadata Fields

Specimen part, Cell line

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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