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accession-icon GSE109803
Gene expression profiling of Hodgkin Lymphoma and Non-Hodgkin Lymphoma cell lines for the NF-kB family of trasncription factors followinf each one depletion by shRNA.
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

NF-kB transcription factors regulate different sets of genes in distinct germinal center derived B-cell lymphomas

Publication Title

No associated publication

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE107613
Gene expression profile of juvenile R6/1 and N171-82Q brains
  • organism-icon Mus musculus
  • sample-icon 54 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Transcriptional dysregulation in Huntingtons disease (HD) is an early event that affects the expression of genes involved in survival and neuronal functions throughout the progression of the pathology. In the last years, extensive research has focused on epigenetic and chromatin-modifying factors as a causative explanation for such dysregulation, offering attractive targets for pharmacological therapies. In this work we examined the gene expression profiles in cortex, striatum, hippocampus and cerebellum of juvenile R6/1 and N171-82Q mice, two models of fast progressive HD, to retrieve the early transcriptional signatures associated with this pathology.These profiles showed significant coincidences with the transcriptional changes in the conditional knockout for the lysine acetyltransferase CBP in postmitotic forebrain neurons.

Publication Title

Early alteration of epigenetic-related transcription in Huntington's disease mouse models.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE44306
Gene expression profile of N171-HD82Q hippocampus and cerebellum.
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Transcriptional dysregulation is an important early feature of polyglutamine diseases. One of its proposed causes is defective neuronal histone acetylation, but important aspects of this hypothesis, such as the precise genomic topography of acetylation deficits

Publication Title

Genomic landscape of transcriptional and epigenetic dysregulation in early onset polyglutamine disease.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE21137
Ultrastructural and transcriptional profiling of neuropathological misregulation of CREB function
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

We compare here the neurodegenerative processes observed in the hippocampus of bitransgenic mice with chronically altered levels of cAMP-response element-binding protein (CREB) function. The combination of genome-wide transcriptional profiling of degenerating hippocampal tissue with microscopy analyses reveals that the sustained inhibition of CREB function in A-CREB mice is associated with dark neuron degeneration, whereas its strong chronic activation in VP16-CREB mice primarily causes excitotoxic cell death and inflammation. Furthermore, the meta-analysis with gene expression profiles available in public databases identifies relevant common markers to other neurodegenerative processes and highlights the importance of the immune response in neurodegeneration. Overall, these analyses define the ultrastructural and transcriptional signatures associated with these two forms of hippocampal neurodegeneration, confirm the importance of fine-tuned regulation of CREBdependent gene expression for CA1 neuron survival and function, and provide novel insight into the function of CREB in the etiology of neurodegenerative processes.

Publication Title

No associated publication

Sample Metadata Fields

Age

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accession-icon GSE14320
Basal and kainate-induced gene expression in A-CREB mouse hippocampi
  • organism-icon Mus musculus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The cAMP responsive element binding protein (CREB) pathway has been involved in two major cascades of gene expression regulating neuronal function. The first one presents CREB as a critical component of the molecular switch that control longlasting forms of neuronal plasticity and learning. The second one relates CREB to neuronal survival and protection. To investigate the role of CREB-dependent gene expression in neuronal plasticity and survival in vivo, we generated bitransgenic mice expressing A-CREB, an artificial peptide with strong and broad inhibitory effect on the CREB family, in forebrain neurons in a regulatable manner. The expression of ACREB in hippocampal neurons impaired L-LTP, reduced intrinsic excitability and the susceptibility to induced seizures, and altered both basal and activity-driven gene expression. In the long-term, the chronic inhibition of CREB function caused severe loss of neurons in the CA1 subfield as well as in other brain regions. Our experiments confirmed previous findings in CREB deficient mutants and revealed new aspects of CREB-dependent gene expression in the hippocampus supporting a dual role for CREB-dependent gene expression regulating intrinsic and synaptic plasticity and promoting neuronal survival. manufacturer's protocol.

Publication Title

Inhibition of cAMP response element-binding protein reduces neuronal excitability and plasticity, and triggers neurodegeneration.

Sample Metadata Fields

Age, Treatment

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accession-icon GSE43290
Expression data from meningiomas and normal meninges
  • organism-icon Homo sapiens
  • sample-icon 51 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Correlate the gene expression profiles with the most relevant patterns of chromosome abnormalities (cytogenetic subgroups of meningiomas) and the gene expression profiles could help to explain the differences in clinical behaviour of meningiomas.

Publication Title

Gene expression profiles of meningiomas are associated with tumor cytogenetics and patient outcome.

Sample Metadata Fields

Sex, Age, Disease stage

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accession-icon GSE43289
Gene expression profiles of gliomas with Affymetrix Human Genome U133 Plus 2.0 Array
  • organism-icon Homo sapiens
  • sample-icon 32 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Correlate the gene expression profiles with the most relevant patterns of chromosome abnormalities (cytogenetic subgroups of gliomas) and the histopathology.

Publication Title

Gene expression profiles of human glioblastomas are associated with both tumor cytogenetics and histopathology.

Sample Metadata Fields

Sex, Age, Disease stage

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accession-icon GSE22971
Expression data from MMP-8 wild type and KO mice with or without arthritis
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Rheumatoid arthritis is an autoimmune disease in which joint inflammation lead to progressive cartilage and bone destruction. Matrix metalloproteinases (MMP) implicated in homeostasis of extracellular matrix (ECM) play a central role in cartilage degradation. The aim of this study was to investigate the role of MMP-8 (collagenase-2) suppression in the K/BxN serum-transfer arthritis model.

Publication Title

Matrix metalloproteinase-8 deficiency increases joint inflammation and bone erosion in the K/BxN serum-transfer arthritis model.

Sample Metadata Fields

Specimen part

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accession-icon GSE72269
Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Disease stage

View Samples
accession-icon GSE138402
Differentially expressed noncoding RNAs as potential biomarkers for DIPG diagnosis and prognosis
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

The most fatal primary brainstem tumors in pediatric patients are diffuse intrinsic pontine gliomas (DIPGs). The identification of genetic alterations, such as the H3K27M mutation, allows a better molecular classification of these tumors. Therefore, the identification of new molecular features, mediating their formation and progression, as non-coding RNAs (ncRNAs), would be of great importance for the development of effective treatments.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part, Disease

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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