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accession-icon SRP127007
The spatial position of budding yeast chromosomes affects gene expression
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 35 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects is still controversial. To determine how changes in chromosome positioning affect transcription we characterized nuclear organization and global gene expression after large-scale chromosomal rearrangements in budding yeast. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. Chromosome displacement relative to the nuclear periphery has mild but widespread and significant effects on transcription. Our study suggests that basal transcriptional activity is sensitive to radial changes on chromosomal position, and provides support for the functional relevance of budding yeast chromosome-level 3D organization in gene expression. Overall design: We analysed 42 samples in total: wildtype (409) strain (4 replicas), mutant strain 524 (4 replicas), mutant strain 527 (4 replicas), mutant strain 1138 (4 replicas), mutant strain 1228 (4 replicas), mutant strain 1379 (4 replicas), mutant strain 1387 (4 replicas), mutant strain 1380 (4 replicas), mutant strain 1388 (4 replicas), mutant strain 1788 (3 replicas), mutant strain 1793 (3 replicas)

Publication Title

Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE84992
Expression data from human primary skeletal muscle myotubes treated with aldosterone alone or in combination
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Gene expression effects of glucocorticoid and mineralocorticoid receptor agonists and antagonists on normal human skeletal muscle.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE84990
Expression data from human primary skeletal muscle myotubes treated with aldosterone, spironolactone, eplerenone, mifepristone, prednisolone or vehicle
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

To define the direct gene expression changes in normal human skeletal muscle with mineralocorticoid and glucocorticoid receptor agonist and antagonist treatment.

Publication Title

Gene expression effects of glucocorticoid and mineralocorticoid receptor agonists and antagonists on normal human skeletal muscle.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE84991
Expression data from human primary skeletal muscle myotubes treated with aldosterone alone or co-incubated with aldosterone plus spironolactone, eplerenone, or mifepristone
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

To uncover whether aldosterone induces gene expression changes through mineralocorticoid or glucocorticoid receptors and determine if eplerenone and spironolactone could block aldosterone induced gene expression to the same extent

Publication Title

Gene expression effects of glucocorticoid and mineralocorticoid receptor agonists and antagonists on normal human skeletal muscle.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE8421
Gene Expression Profile in Rat Adrenal Zona Glomerulosa Cells Stimulated with Aldosterone Secretagogues
  • organism-icon Rattus norvegicus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

The mineralocorticoid aldosterone mainly produced by the adrenal gland is essential for life but an abnormal excessive secretion causes severe pathological effects including hypertension and target organ injury in the heart and kidney. The aim of this study was to determine the gene regulatory network triggered by aldosterone secretagogues in a non transformed cell system. Freshly isolated rat adrenal zona glomerulosa cells were stimulated with the two main aldosterone secretagogues, angiotensin II and potassium, for two hours and subjected to whole genome expression studies using multiple biological and bioinformatics tools. Several genes were differentially expressed by Ang II (n=133) or potassium (n=216). Genes belonging to the nucleic acid binding and transcription factor activity categories were significantly enriched. A subset of the most regulated genes were confirmed by real-time RT-PCR and then their expression analyzed in time curve studies. Differentially expressed genes were grouped according to their time-response expression pattern and their promoter regions analyzed for common regulatory transcription factors binding sites. Finally, data mining with gene promoters, transcription factors and literature databases were performed to generate gene interaction networks for either Ang II or potassium. This study provides for the first time a complete study of the genes that are regulated, and the interaction between them, by aldosterone secretagogues in rat adrenal cells. Increasing our knowledge of adrenal physiology and gene regulation in non transformed cell systems would lead us to a better approach for discovery of candidate genes involved pathological conditions of the adrenal cortex.

Publication Title

Gene expression profile in rat adrenal zona glomerulosa cells stimulated with aldosterone secretagogues.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE18842
Gene expression analysis of human lung cancer and control samples
  • organism-icon Homo sapiens
  • sample-icon 91 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

PURPOSE

Publication Title

Gene expression profiling reveals novel biomarkers in nonsmall cell lung cancer.

Sample Metadata Fields

Specimen part, Disease

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accession-icon GSE70822
Expression data from human primary skeletal muscle myotubes treated with aldosterone, spironolactone, or vehicle.
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

To test for a function effect of mineralocorticoid receptor modulation in skeletal muscle, global gene expression analysis was conducted on human myltubes treated with a mineralocorticoid receptor agonist or antagonist.

Publication Title

Mineralocorticoid receptors are present in skeletal muscle and represent a potential therapeutic target.

Sample Metadata Fields

Sex

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accession-icon GSE70984
Expression data from quadriceps of utrn+/-;mdx mice treated with spironolactone plus lisinopril compared to untreated
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

To identify the gene expression differences in skeletal muscles resulting from treatment of dystrophic mice with spironolactone plus lisinopril

Publication Title

Mineralocorticoid receptors are present in skeletal muscle and represent a potential therapeutic target.

Sample Metadata Fields

Sex, Age, Treatment

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accession-icon GSE10810
Gene expression signatures in breast cancer distinguish phenotype charact., histological subtypes, and tumor invasivness
  • organism-icon Homo sapiens
  • sample-icon 56 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Background. The development of reliable gene expression profiling technology is having an increasing impact on our understanding of breast cancer biology.

Publication Title

Gene expression signatures in breast cancer distinguish phenotype characteristics, histologic subtypes, and tumor invasiveness.

Sample Metadata Fields

Disease stage

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accession-icon GSE37458
Expression data from WT and VAChT KDHOM ventricles
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

VAChT KDHOM mice have a 70% decrease in the vesicular acetylcholine transporter (VAChT) and this leads to a systemic decrease in ACh release and cardiac dysfunction.

Publication Title

An analysis of the myocardial transcriptome in a mouse model of cardiac dysfunction with decreased cholinergic neurotransmission.

Sample Metadata Fields

Sex, Age, Specimen part

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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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