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accession-icon GSE27041
OXPHOS complex I deficiency leads to transcriptional changes of the Nrf2-Keap1 pathway and selenoproteins.
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Defective complex I (CI) is the most common type of oxidative phosphorylation (OXPHOS) disease in patients, with an incidence of 1 in 5,000 live births. Complex I deficiency can present in infancy or early adulthood and shows a wide variety of clinical manifestations, including Leigh syndrome, (cardio)myopathy, hypotonia, stroke, ataxia and lactic acidosis. A number of critical processes and factors, like superoxide production, calcium homeostasis, mitochondrial membrane potential and mitochondrial morphology, are known to be involved in clinical CI deficiency, but not all factors are yet known and a complete picture is lacking.

Publication Title

Transcriptional changes in OXPHOS complex I deficiency are related to anti-oxidant pathways and could explain the disturbed calcium homeostasis.

Alternate Accession IDs

E-GEOD-27041

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

View Samples
accession-icon GSE41410
Co-expression of genes with ERG in prostate cancers and cell lines
  • organism-icon Homo sapiens
  • sample-icon 65 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer.

Alternate Accession IDs

E-GEOD-41410

Sample Metadata Fields

Cell line

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accession-icon GSE41408
Co-expression of genes with ERG in prostate cancers
  • organism-icon Homo sapiens
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene.

Publication Title

Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer.

Alternate Accession IDs

E-GEOD-41408

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE59745
Identification of novel long non-coding RNAs in prostate cancers
  • organism-icon Homo sapiens
  • sample-icon 42 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

Long non-coding RNAs show highly tissue and disease specific expression profiles. We analyzed prostate cancer and normal adjacent prostate samples to identify cancer-specific transcripts and found 334 candidates, of which 15 were validated by RT-PCR.

Publication Title

Novel long non-coding RNAs are specific diagnostic and prognostic markers for prostate cancer.

Alternate Accession IDs

E-GEOD-59745

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE41407
Co-expression of genes with ERG in prostate cancer cell lines
  • organism-icon Homo sapiens
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene.

Publication Title

Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer.

Alternate Accession IDs

E-GEOD-41407

Sample Metadata Fields

Cell line

View Samples
accession-icon GSE16659
Expression data of HGF/cMET pathway in prostate cancer DU145 cell line
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

DU145 prostate cancer cells were treated with 25 ng/ml hepatocyte growth factor (HGF) or vehicle for 2, 8, or 24 hours. HGF stimulates the cMET protein, a tyrosine kinase transmembrane protein.

Publication Title

Activation of c-MET induces a stem-like phenotype in human prostate cancer.

Alternate Accession IDs

E-GEOD-16659

Sample Metadata Fields

Cell line, Time

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accession-icon GSE4286
Making a predictive heart failure expression profile in Ren2 rat left ventricles
  • organism-icon Rattus norvegicus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

The intercalated disc of cardiac myocytes is emerging as a crucial structure in the heart. Loss of intercalated disc proteins like N-cadherin causes lethal cardiac abnormalities, mutations in intercalated disc proteins cause human cardiomyopathy. A comprehensive screen for novel mechanisms in failing hearts demonstrated that expression of the lysosomal integral membrane protein-2 (LIMP-2) is increased in cardiac hypertrophy and heart failure in both rat and human myocardium. Complete loss of LIMP-2 in genetically engineered mice did not affect cardiac development; however these LIMP-2 null mice failed to mount a hypertrophic response to increased blood pressure but developed cardiomyopathy. Disturbed cadherin localization in these hearts suggested that LIMP-2 has important functions outside lysosomes. Indeed, we also find LIMP-2 in the intercalated disc, where it associates with cadherin. RNAi-mediated knockdown of LIMP-2 decreases the binding of phosphorylated b-catenin to cadherin, while overexpression of LIMP-2 has the opposite effect. Taken together, our data show that lysosomal integrated membrane protein-2 is crucial to mount the adaptive hypertrophic response to cardiac loading. We demonstrate a novel role for LIMP-2 as an important mediator of the intercalated disc.

Publication Title

Lysosomal integral membrane protein 2 is a novel component of the cardiac intercalated disc and vital for load-induced cardiac myocyte hypertrophy.

Alternate Accession IDs

E-GEOD-4286

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE58952
IL-37 protects against obesity-induced inflammation and insulin resistance
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.1 ST Array (mogene11st)

Description

Cytokines of the IL-1 family are important modulators of obesity-induced inflammation and the development of systemic insulin resistance. Here, we report that IL-37, a newly-described antiinflammatory member of the IL-1 family, affects obesity-induced inflammation and insulin resistance. IL-37 transgenic mice (IL-37tg) did not develop an obese phenotype in response to a high-fat diet (HFD). Unlike WT mice, IL-37tg mice exhibited reduced numbers of adipose tissue macrophages and preserved glucose tolerance and insulin sensitivity after 16 weeks of HFD. A short-term HFD intervention revealed that the IL-37-mediated improvement in glucose tolerance is independent of bodyweight. IL-37tg mice manifested a beneficial metabolic profile with higher circulating levels of the anti-inflammatory adipokine adiponectin. In vitro treatment of differentiating adipocytes with recombinant IL-37 reduced adipogenesis. The beneficial effects of recombinant IL-37 involved activation of AMPK signaling. In humans, steady-state IL-37 adipose tissue mRNA levels were positively correlated with insulin sensitivity, lower adipose tissue levels of leptin and a lower inflammatory status of the adipose tissue. These findings reveal IL-37 as an important anti-inflammatory modulator during obesity-induced inflammation and insulin resistance in both mice and humans and suggest that IL-37 is a potential target for the treatment of obesity-induced insulin resistance and type 2 diabetes.

Publication Title

IL-37 protects against obesity-induced inflammation and insulin resistance.

Alternate Accession IDs

E-GEOD-58952

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP075061
Transcriptome analysis in HT29 and SW480 cells depleted of Prdx2
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Prdx2 is the thioredoxin-dependent peroxidase that reduces H2O2 using reducing power NADPH in the presence of thioredoxin and thioredoxin reductase. Prdx2 plays an important role in growth. factor signaling in mammlian cells. Therefore, we examined the gene expression in colon adenocarcinoma cell line HT29 after Prdx2 depletion. Prdx2 depletion resulted in a significant alteration on gene expression, including protein synthesis, metabolisms, and cell cycle. Overall design: Control-siRNA-transfected versus PRDX2-siRNA-transfected HT29 and SW480 cells

Publication Title

Interaction of tankyrase and peroxiredoxin II is indispensable for the survival of colorectal cancer cells.

Alternate Accession IDs

GSE81429

Sample Metadata Fields

Cell line, Subject

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accession-icon SRP124875
A facile method for generating tumorigenic cancer stem cell spheroids from diverse cancer cell lines
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Although cancer stem cells (CSCs) are thought to be responsible for tumor recurrence and resistance to chemotherapy, CSC-related research and drug development have been hampered by the limited supply of patient-derived diverse CSCs. Here, we developed a functional polymer thin film (PTF) platform that promotes conversion of human cancer cell lines to highly tumorigenic spheroids without the use of biochemical or genetic manipulations. Culturing various human cancer cells on the specific PTF, poly(2,4,6,8-tetravinyl-2,4,6,8-tetramethyl cyclotetrasiloxane) (pV4D4), gave rise to numerous multicellular spheroids within 24 hours, with high efficiency and reproducibility. Cancer cells in the resulting spheroids showed an enormous increase in the expression of CSC-associated genes and acquired dramatically increased drug resistance compared with monolayer-cultured controls. These spheroids also showed greatly enhanced xenograft tumor-forming ability and metastasis capacity in nude mice. By enabling the generation of tumorigenic spheroids as a patient-derived CSC substitute, the surface platform described here will likely contribute to CSC-related basic research and drug development. Overall design: mRNA profiles of 8 day-SKOV3-ssiCSC spheroids and 2D-cultured SKOV3 control were generated by deep sequencing, in duplicate, using Hiseq-2500.

Publication Title

Polymer Thin Film-Induced Tumor Spheroids Acquire Cancer Stem Cell-like Properties.

Alternate Accession IDs

GSE106848

Sample Metadata Fields

Specimen part, Subject

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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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