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accession-icon GSE140599
Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats
  • organism-icon Rattus norvegicus
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconIllumina ratRef-12 v1.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genetic Liability for Internalizing Versus Externalizing Behavior Manifests in the Developing and Adult Hippocampus: Insight From a Meta-analysis of Transcriptional Profiling Studies in a Selectively Bred Rat Model.

Sample Metadata Fields

Sex, Specimen part, Treatment

View Samples
accession-icon GSE140594
Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: Illumina Microarray Data from Generation F15
  • organism-icon Rattus norvegicus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina ratRef-12 v1.0 expression beadchip

Description

The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This Illumina (RatRef-12v1 Beadchip) microarray study examined gene expression in the hippocampus in generation F15 male bHR rats and bLR rats at age postnatal day 14 (P14, n=6 per group).

Publication Title

Genetic Liability for Internalizing Versus Externalizing Behavior Manifests in the Developing and Adult Hippocampus: Insight From a Meta-analysis of Transcriptional Profiling Studies in a Selectively Bred Rat Model.

Sample Metadata Fields

Sex, Specimen part

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accession-icon SRP064345
RNA-Seq profiling of Ewing''s sarcoma and MSC cell lines
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

Comparison of expression profile of Ewing''s sarcoma with cell of origin, mesenchymal stem cells with the goal of identifying novel therapeutic targets. Overall design: 3 Ewing''s cell lines compared to 2 MSC cell lines

Publication Title

Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE7269
AJ mouse lung carcinogenesis study
  • organism-icon Mus musculus
  • sample-icon 29 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A macrophage gene expression signature defines a field effect in the lung tumor microenvironment.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE7258
Expression data of bronchoalveolar lavage cells from control or urethane treated AJ mice
  • organism-icon Mus musculus
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

AJ mouse is susceptible to lung carcinogenesis from urethane treatment and is a good model for human adenocarcinoma. We completed a study using microarray analysis of bronchoalveolar lavage cells from control or urethane treated mice. A unique macrophage expression signature in the lung tumor microenvironment was able to correctly classify the lavage samples.

Publication Title

A macrophage gene expression signature defines a field effect in the lung tumor microenvironment.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-2058
Transcription profiling by array of Xenopus embryos after treatment with dominant negative FGF receptor 1 or 4
  • organism-icon Xenopus laevis
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Xenopus laevis Genome Array (xenopuslaevis)

Description

Genes regulated by the fibroblast growth factor (FGF) signalling pathway were indentified in the early development of the amphibian Xenopus laevis by comparing gene expression in control embryos and embryos in which FGF signalling was inhibited by two different dominant negative FGF receptors.

Publication Title

Characterisation of the fibroblast growth factor dependent transcriptome in early development.

Sample Metadata Fields

Age, Compound, Time

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accession-icon GSE93527
Expression analysis of human TAG2 primary bladder tumours
  • organism-icon Homo sapiens
  • sample-icon 35 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Expression data derived from this analysis was used to compare expression signatures between genomic subgroups identified from DNA copy number analysis.

Publication Title

Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency.

Sample Metadata Fields

Sex, Age

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accession-icon GSE32529
Mouse ischemic tolerance genomic analysis of the brain and blood.
  • organism-icon Mus musculus
  • sample-icon 224 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Ischemic tolerance can be induced by numerous preconditioning stimuli, including various Toll-like receptor (TLR) ligands. We have shown previously that systemic administration of the TLR4 ligand, lipopolysaccharide (LPS) or the TLR9 ligand, unmethylated CpG ODNs prior to transient brain ischemia in mice confers substantial protection against ischemic damage. To elucidate the molecular mechanisms of preconditioning, we compared brain and blood genomic profiles in response to preconditioning with these TLR ligands and to preconditioning via exposure to brief ischemia.

Publication Title

Multiple preconditioning paradigms converge on interferon regulatory factor-dependent signaling to promote tolerance to ischemic brain injury.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE79598
Expression data from H9 human embryonic stem cells (hESCs) infected with either lentiviral non-silencing shRNA or shRUNX1, and differentiated to early mesendoderm
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

We used microarrays to detail the global program of gene expression during early hESC differentiation to mesendoderm using FBS, with and without RUNX1 depletion.

Publication Title

Transient RUNX1 Expression during Early Mesendodermal Differentiation of hESCs Promotes Epithelial to Mesenchymal Transition through TGFB2 Signaling.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE95250
Early Induction of NRF-2 Antioxidant Pathway by RHBDF2 Mediates More Rapid Cutaneous Healing in Mice
  • organism-icon Mus musculus
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Rhomboid family protein RHBDF2, an upstream regulator of the epidermal growth factor (EGF) receptor signaling, has been implicated in cutaneous wound healing. However, the underlying molecular mechanisms are still emerging. Using a gain-of-function mutation in the mouse Rhbdf2 gene (Rhbdf2cub/cub), which shows a regenerative phenotype, we sought to identify the underlying mechanism.

Publication Title

Early induction of NRF2 antioxidant pathway by RHBDF2 mediates rapid cutaneous wound healing.

Sample Metadata Fields

Specimen part, Treatment, Time

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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