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accession-icon GSE36868
Simvastatin treated Lymphoblastoid Cell lines from Cholesterol and Pharmacogenomics (CAP) Trial
  • organism-icon Homo sapiens
  • sample-icon 960 Downloadable Samples
  • Technology Badge IconIllumina HumanRef-8 v3.0 expression beadchip

Description

Statins reduce cardiovascular disease risk by lowering plasma low density lipoprotein (LDL)-cholesterol. To identify novel pathways that modulate statin response, we assessed the influence of simvastatin exposure on expression quantitative trait locus (eQTL) associations across the genome in 480 lymphoblastoid cell lines (LCLs). Cell lines were derived blood samples collected ant entry visit from participants in the Cholesterol and Pharmacogenomics (CAP) trial, who underwent a 6 week 40mg/day simvastatin trial. We identified 4590 cis-eQTLS that were independent of treatment status (FDR=1%) and six cis-eQTLS for which there was evidence of an interaction with treatment (FDR=20%). Genotypes and Phenotypes derived from these indivudals are available through dbGaP (Accession Number). eQTL results are available at: http://eqtl.uchicago.edu/cgi=bin/gbrowse/eqtl/

Publication Title

HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism.

Alternate Accession IDs

E-GEOD-36868

Sample Metadata Fields

Sex, Subject

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accession-icon GSE4174
Effect of Sleep Deprivation on the Whole Brain of Drosophila
  • organism-icon Drosophila melanogaster
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

To gain insight into the dynamic molecular processes that are altered during prolonged wakefulness and during sleep. We performed an RNA expression profiling study examining temporal changes in the brain of Drosophila in relationship to the duration of prior sleep or wakefulness. Our experimental design allowed us to determine whether genes identified as differentially regulated between sleep and wakefulness were up- or down-regulated in these states.

Publication Title

Multiple mechanisms limit the duration of wakefulness in Drosophila brain.

Alternate Accession IDs

E-GEOD-4174

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
accession-icon GSE6514
Gene expression in the mouse brain during spontaneous sleep and prolonged wakefulness
  • organism-icon Mus musculus
  • sample-icon 90 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

These studies address temporal changes in gene expression during spontaneous sleep and extended wakefulness in the mouse cerebral cortex, a neuronal target for processes that control sleep; and the hypothalamus, an important site of sleep regulatory processes. We determined these changes by comparing expression in sleeping animals sacrificed at different times during the lights on period, to that in animals sleep deprived and sacrificed at the same diurnal time.

Publication Title

Macromolecule biosynthesis: a key function of sleep.

Alternate Accession IDs

E-GEOD-6514

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE95214
Ventral prostate in male F344 rats: Control vs. PhIP treatment
  • organism-icon Rattus norvegicus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

The gene expression profling between Control and 300 mg/kg PhIP treatment in ventral prostate lobe of male F344 rats

Publication Title

Early detection of prostate carcinogens by immunohistochemistry of HMGB2.

Alternate Accession IDs

E-GEOD-95214

Sample Metadata Fields

Specimen part

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accession-icon GSE46749
Effect of vitamin D on gene expression in human alveolar type II cells
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

To test whether vitamin D has a functionally important effect upon primary alveolar epithelial type II cells we used gene expression microarray to identify genes that are regulated by 25-dihydroxyvitamin D in adult alveolar type II cells.

Publication Title

Vitamin D deficiency contributes directly to the acute respiratory distress syndrome (ARDS).

Alternate Accession IDs

E-GEOD-46749

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE70526
Expression data from plant tissues during incompatible interaction between the rice host and its major pest, the Asian rice gall midge
  • organism-icon Oryza sativa
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

During an incompatible or compatible interaction between rice (Oryza sativa) and the Asian rice gall midge (Orseolia oryzae), a lot of genetic reprogamming occurs in the plant host

Publication Title

Metabolic and transcriptomic changes induced in host during hypersensitive response mediated resistance in rice against the Asian rice gall midge.

Alternate Accession IDs

E-GEOD-70526

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE48284
Gene expression of SKOV3 cells after no treatment or treatment with 50 microM peracetylated GlcNAc or peracetylated 4-deoxy-GlcNAc for three days
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Heparan sulfate (HS), a long linear polysaccharide, is implicated in various steps of tumorigenesis, including angiogenesis. We successfully interfered with HS biosynthesis using a peracetylated 4-deoxy analog of the HS constituent GlcNAc and studied the compounds metabolic fate and its effect on angiogenesis. The 4-deoxy analog was activated intracellularly into UDP-4-deoxy-GlcNAc and HS expression was inhibited up to ~96% (IC50 = 16 M). HS chain size was reduced, without detectable incorporation of the 4-deoxy analog, likely due to reduced levels of UDP-GlcNAc and/or inhibition of glycosyltransferase activity. Comprehensive gene expression analysis revealed reduced expression of genes regulated by HS binding growth factors as FGF-2 and VEGF. Cellular binding and signaling of these angiogenic factors was inhibited. Micro-injection in zebrafish embryos strongly reduced HS biosynthesis, and angiogenesis was inhibited in both zebrafish and chicken model systems. All these data identify 4-deoxy-GlcNAc as a potent inhibitor of HS synthesis which hampers pro-angiogenic signaling and neo-vessel formation.

Publication Title

Interfering with UDP-GlcNAc metabolism and heparan sulfate expression using a sugar analogue reduces angiogenesis.

Alternate Accession IDs

E-GEOD-48284

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE9247
Effect of histone deacetylase inhibitors on osteoblast gene expression
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Background:

Publication Title

Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors.

Alternate Accession IDs

E-GEOD-9247

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE27393
Gene expression in lungs from male HIV transgenic rats
  • organism-icon Rattus norvegicus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

HIV Tg rats exhibit pulmonary hypertension and pulmonary artery remodeling. In an effort to begin to understand cell signaling pathways which are altered in lungs from HIV transgenic rats, we used microarray analysis.

Publication Title

Human immunodeficiency virus transgenic rats exhibit pulmonary hypertension.

Alternate Accession IDs

E-GEOD-27393

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE47967
Cooperation of estrogen and oocytes on gene expression in mouse cumulus cells
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Oocyte-derived paracrine factors and estrogens cooperate to regulate the function and development of mouse cumulus cells.

Publication Title

Cooperative effects of 17β-estradiol and oocyte-derived paracrine factors on the transcriptome of mouse cumulus cells.

Alternate Accession IDs

E-GEOD-47967

Sample Metadata Fields

Sex, Specimen part, Treatment

View Samples
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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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