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accession-icon GSE26809
FMRP Associates with Polyribosomes
  • organism-icon Mus musculus
  • sample-icon 26 Downloadable Samples
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Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE26745
Comparison of total and polyribosome-associated mRNA levels in male Fmr1 KO mice and male WT littermates
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
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Description

The Fragile X Mental Retardation Protein, FMRP, is thought to regulate the translation of a specific set of neuronal mRNAs on polyribosomes. Therefore, we prepared polyribosomes on sucrose gradients and purified mRNA specifically from these fractions, as well as the total mRNA levels, to determine whether a set of mRNAs might be changed in its % association with polyribosomes in the absence of FMRP in the KO mouse model.

Publication Title

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE17667
Pou5f1 transcription targets in zebrafish
  • organism-icon Danio rerio
  • sample-icon 3 Downloadable Samples
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Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE17657
Experiment 4: Affymetrix validation array
  • organism-icon Danio rerio
  • sample-icon 3 Downloadable Samples
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Description

Zebrafish embryo were analyzed at 30 and 60 % epiboly for changes in transcriptome of wild-type and MTspg mutant embryos

Publication Title

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE16801
Comparative gene expression analysis of 2 subpopulations of dermal papilla cells.
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
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Description

Different types of hair follicles can be found in the skin of mice. It is believed that the signals that control hair follicle differentiation arise from cells in a structure called the dermal papilla. Understanding the nature of those signals is of interest for the biology of the normal tissue.

Publication Title

Sox2-positive dermal papilla cells specify hair follicle type in mammalian epidermis.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE83196
Beta-catenin-regulated genes in pancreatic cancer cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
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Description

Activation of the canonical Wnt signaling pathway is commonly observed in pancreatic cancer. We therefore sought to identify a gene expression profile associated with the activation of this pathway in pancreatic cancer cells.

Publication Title

Activation of WNT/β-Catenin Signaling Enhances Pancreatic Cancer Development and the Malignant Potential Via Up-regulation of Cyr61.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE55883
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
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Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrative cross-omics analysis in primary mouse hepatocytes unravels mechanisms of cyclosporin A-induced hepatotoxicity.

Sample Metadata Fields

Specimen part

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accession-icon GSE55881
Expression Profiles of Primary Mouse Hepatocytes treated with Cyclosporin A and solvent control [RNA]
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon

Description

The transcriptomics changes induced in Primary Mouse Hepatocytes by Cyclosporin A after treatment for 24h and 48h

Publication Title

Integrative cross-omics analysis in primary mouse hepatocytes unravels mechanisms of cyclosporin A-induced hepatotoxicity.

Sample Metadata Fields

Specimen part

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accession-icon GSE6134
Offsprings of crosses between hypercholesterolemic and normocholesterolemic parents LUMC-HKG-ApoE-Atherosclerosis
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
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Description

Enhanced prenatal fatty streak formation in human fetuses has been associated with maternal hypercholesterolemia. However, the possible roles of maternal genetic background and in utero environment on development of atherosclerosis in adult life have not been unraveled. We generated genetically identical heterozygous apoE-deficient mice offspring with a different maternal background to study the intrauterine effect of maternal genotype and associated hypercholesterolemia on the developing vascular system. As read out for increased atherosclerosis development in adult life, a constrictive collar was placed around the carotid artery to induce lesion formation. A significant increase in endothelial cell activation and damage was detected in the carotid arteries of heterozygous apoE-deficient fetuses with apoE-deficient mothers compared with offspring from wild type mothers, but no fatty streak formation was observed. Postnatally, all carotid arteries revealed normal morphology. In adult offspring with maternal apoE-deficiency, the constrictive collar resulted in severe lesion (9/10) development compared with no to only minor lesions (2/10) in offspring of wild type mothers. Microarray analysis showed no effect of maternal apoE-deficiency on gene expression in adult offspring. We conclude that maternal apoE-deficiency not only affects fetal arteries, but also increases the susceptibility for development of collar-induced atherosclerosis in adult life.

Publication Title

Intrauterine exposure to maternal atherosclerotic risk factors increases the susceptibility to atherosclerosis in adult life.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE21048
Prednisolone-induced differential gene expression in liver of mice carrying the wild type or a dimerization-defective glucocorticoid receptor
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon

Description

Glucocorticoids control expression of a large number of genes after binding to the glucocorticoid receptor (GR). Transcription may be regulated either by binding of the GR dimer to DNA regulatory elements or by protein-protein interactions of GR monomers with other transcription factors. Although the type of regulation for a number of individual target genes is known, the relative contribution of both mechanisms to the regulation of the entire transcriptional program remains elusive.

Publication Title

Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.

Sample Metadata Fields

Sex, 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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