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accession-icon GSE99199
Pharmacogenomic comparison between D3T- and CDDO-Im in mouse liver tissue
  • organism-icon Mus musculus
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The Keap1/Nrf2 signaling pathway is a tractable target for the pharmacological prevention of tumorigenesis. 3H-1,2-dithiole-3-thione (D3T) and 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im) are representative members of two classes of Nrf2-activating chemopreventive agents. Natural dithiolethiones have been widely used in clinical trials for cancer chemoprevention. Synthetic triterpenoids, however, have been shown to be significantly more potent Nrf2 activators and are under clinical evaluation for the treatment of chronic kidney disease. This study seeks to characterize the structure-activity relationship between D3T and CDDO-Im in mouse liver tissue. To this end we treated Wt and Nrf2-null mice with 300 umol/kg bw D3T and 3, 10, and 30 umol/kg bw CDDO-Im every other day for 5 days and evaulated global gene expression changes as a product of both treamtent and genotype using Affymetrix microarray.

Publication Title

Pharmacogenomics of Chemically Distinct Classes of Keap1-Nrf2 Activators Identify Common and Unique Gene, Protein, and Pathway Responses In Vivo.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE8880
Analyzing microarray data with transitive directed acyclic graphs
  • organism-icon Rattus norvegicus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Test compound one, 5,6-benzoflavone (BNF), was known to act through both the Ah receptor and Nrf2 receptor pathways, while test compounds two and three, 3H-1,2-dithiole-3-thione (D3T) and 4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thione (OLT), were known to act through the Nrf2 receptor pathway. Furthermore, D3T is known to be more potent and efficacious than OLT for Nrf2 activation. OLT has been shown to exhibit 20-50% of the efficacy of D3T for inhibition of alfatoxin-induced heptic foci. Nonetheless, because OLT is an approved drug, it is currently being evaluated in human phase II intervention trials of biomarkers of alfatoxin-related hepatocellular carcinoma. More recently, BNF was shown to be an effective chemopreventive agent in the rat mammary carcinogen model, inhibiting 7,12-dimethylbenz(a)anthracene DNA adduct formation in liver and mammary cells by 96 and 83% respectively.

Publication Title

Analyzing microarray data with transitive directed acyclic graphs.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE32217
Expression data from normal human epidermal keratinocytes undergoing density-induced differentiation and treated with EGF
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Combining genome-wide microarray and functional analyses, we found that EGFR activation abrogates barrier function, increasing transepidermal water loss (TEWL) and transepithelial permeability of water-soluble ions and higher molecular weight dextrans, in part by disrupting the expression of tight junction proteins. EGF decreases certain lipid matrix free fatty acids and ceramides by its actions to repress the expression of specific biosynthetic enzymes.

Publication Title

EGFR regulation of epidermal barrier function.

Sample Metadata Fields

Specimen part

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accession-icon GSE19213
Expression data from oxidant treated yeast
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Yeast transcription factor Yap1 mediates adaptive response against H2O2 and the cystein thiol reactive Michael acceptor, N-ethylmaleimid (NEM) and acrolein. The response against H2O2 was found to be distinct from that against NEM and acrolein.

Publication Title

Yap1 activation by H2O2 or thiol-reactive chemicals elicits distinct adaptive gene responses.

Sample Metadata Fields

Treatment

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accession-icon GSE8882
Expression data from livers of rats treated with control, D3T, OLT, or TBD
  • organism-icon Rattus norvegicus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome U34 Array (rgu34a)

Description

The activities of the dithiolethione analogs, D3T, OLT, and TBD are pharmacologically well-understood. These compounds act as chemopreventive agents whose ability is to block or diminish early stages of carcinogenesis. In addition, the three compounds are classified as monofunctional Phase II enzyme inducers and activate the same pathway, namely the Keap1-Nrf2 signal pathway. The three dithiolethiones were showed to ameliorate the AFB1-induced toxicity through increasing phase II enzymes including glutathione S-transferase (GST). The parent D3T was observed to be the most potent chemoprotective agent. Oltipraz, a clinically approved drug, has been shown to exhibit less efficacy than its analogs for inhibition of aflatoxin-induced hepatic foci.TBD was suggested to be better than OLT as a chemopreventive agent because of its reduced toxicity profile.

Publication Title

Chemical genomics of cancer chemopreventive dithiolethiones.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE99064
Exon Level Expression Profiling of Epididymal Adipose Tissue: During Chronic Glucocorticoid Treatment While Consuming an N-6 Rich High Fat Diet
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Transcriptome analysis of total RNA from C57BL/6 epididymal adipose tissue samples

Publication Title

No associated publication

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE36796
Effects of TCDD on differentiating NHEKs
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

TCDD increased expression of numerous differentiation specific genes and decreased expression of numerous genes involved in mitochondrial health and redox homeostasis

Publication Title

2,3,7,8-Tetrachlorodibenzo-p-dioxin-mediated production of reactive oxygen species is an essential step in the mechanism of action to accelerate human keratinocyte differentiation.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE92320
Bio-Electric Field Enhancement: The Influence on MDA-MB231 Cells in Vitro
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

We grew MDA-MB231 cells in a media that had been reconstituted with water that was treated by the Bio-Electric Field Enhancement device generated direct current dielectrophoretic electromagnetic field (Treated group) and cells that were grown in media that was reconstituted with water that was not treated by the BEFE device dc DEP EMF. They were grown for 3 days in each of these media and then analyzed with Affymetrix 2.0 Microarrary Analyses. It was an experimental controlled design.

Publication Title

No associated publication

Sample Metadata Fields

Cell line

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accession-icon GSE7334
Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To better understand the mechanisms involved in aluminum (Al) toxicity and tolerance in plants, microarray technology was used to evaluate changes in gene expression in Arabidopsis thaliana under Al stress. With the use of Affymetrix Arabidopsis ATH1 Genechip, a comparison of RNA expression profiles was made between control and Al-treated Arabidopsis seedlings. A total of 256 genes were identified as Al-responsive. Ninety-four genes were shown to be up-regulated and 162 were down-regulated; comprising 1.1% of the 24,000 Arabidopsis genes. Real-time RT-PCR was used to confirm the microarray data. RNAs associated with known protein functions were classified into categories. The analysis showed that a large number of transcription factors and several putative signaling components were up-regulated by aluminum. Chloroplast structural and photosynthetic genes were, in general, down-regulated. A number of previously identified Al-responsive genes showed similar expression pattern changes in this study. For example, GST, Auxin-regulated, Peroxidase, and Chitinase, were found to be up-regulated by Al-stress, whereas, genes such as Wali 3 and Wali 4, were down-regulated. We also identified several up-regulated genes involved in vacuolar signaling, sorting and docking. Three genes were also up-regulated by Al-stress, Ras GTP-binding protein, ABC-cassette binding, and the AtELP1 receptor genes, have previously been documented as responsive to drought and/or oxidative stress and may play important roles the detoxification of Al ions by transportation and storage into root vacuoles. Ultrastructural changes in the roots tips cells of Arabidopsis were evaluated using TEM and EDXMA with SEM. Results using combined TEM and SEM-EDXMA showed that Al accumulattion in the root tip of Arabidopsis was detectable. The coupling these techniques can be useful for measuring Al in situ in cellular and sub cellular section of plant roots.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE148250
Expression data of TS cells with inactive MAP3K4 (TSKI4 cells) and TSKI4 cells re-expressing REL (TSKI4R cells)
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Trophoblast stem cells lack MAP3K4 activity (TSKI4 cells) switch from epithelial phenotype to intermediate phenotype. Loss of epithelial phenotype is due to the loss of CBP histone acetyltransferase activity and the gain of histone deacetylase HDAC6 expression and activity. In our work, we identify a small network of 183 genes whose expression is co-regulated by MAP3K4, CBP, and HDAC6. Further, we define the key role of one of these co-regulated genes, Rel, in inducing epithelial phenotype in intermediate TSKI4 cells.

Publication Title

Coordinated regulation of Rel expression by MAP3K4, CBP, and HDAC6 controls phenotypic switching.

Sample Metadata Fields

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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