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accession-icon GSE61089
Mouse and rat cells and tissues
  • organism-icon Mus musculus, Rattus norvegicus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE61081
Dilution and amplification control study
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon

Description

Mouse adult female brains cortex (C57BL/6, Charles River Laboratories, Inc.) was isolated and stored immediately at -80C. Subsequently, the mRNA (15g) was isolated using TRIzol Reagent and MicroFastTrack 2.0 Kit (Invitrogen). A Sample of 5g was assessed on Affymetrix Mouse 430.2 array. Aliquots from the leftovers of the same cortical mRNA were diluted to single-cell RNA levels (0.1, 1, and 10 pg) and independently aRNA amplified for a total of 2 and 4 rounds and assessed on Affymetrix Mouse 430.2 arrays.

Publication Title

Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution.

Sample Metadata Fields

Specimen part

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accession-icon GSE17478
Particulate Matter effect on Mouse Model of Cardiac Failure: Lung and Heart Left Ventricle
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon

Description

Particulate Matter Triggers Carotid Body Dysfunction, Respiratory Dysynchrony and Cardiac Arrhythmias in Mice with Cardiac Failure

Publication Title

Particulate matter induces cardiac arrhythmias via dysregulation of carotid body sensitivity and cardiac sodium channels.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE14431
Simvastatin attenuates lung vascular leak and inflammation in a murine model of radiation-induced lung injury
  • organism-icon Mus musculus
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon

Description

Background: Microvascular injury and increased vascular leakage are prominent features of the radiation-induced lung injury (RILI) which follows cancerassociated thoracic irradiation. The mechanisms of RILI are incompletely understood and therapeutic strategies to limit RILI are currently unavailable. We established a murine model of radiation pneumonitis in order to assess mechanism-based therapies for RILI-induced inflammation and vascular barrier dysfunction. Based on prior studies, we investigated the therapeutic potential of simvastatin as a vascular barrier protective agent in RILI.

Publication Title

Simvastatin attenuates radiation-induced murine lung injury and dysregulated lung gene expression.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE10535
Retinal transcripts level alteration in the prCAD -/- mouse, a model for retinal degeneration
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon

Description

This experiment was designed to identify transcripts that exhibit changes in abundance in the context of retinal degeneration by comparing transcript levels in adult wild type and prCAD -/- mouse retinas.

Publication Title

The genomic response to retinal disease and injury: evidence for endothelin signaling from photoreceptors to glia.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE10528
The retinal transcriptional response to light damage
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon

Description

Transcriptional profiles were compared between dark adapted and light damaged BALBc (albino) mouse retinas.

Publication Title

The genomic response to retinal disease and injury: evidence for endothelin signaling from photoreceptors to glia.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE8434
Transcriptional regulation by Errb (Nr3b2) in stria vascularis
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon

Description

Transcriptional profiles were compared in microdissected lateral walls of the inner ears from Errb mutant mice and wild type littermate controls. The goal is to identify transcriptional targets of Errb and candidate genes for inner ear diseases.

Publication Title

Estrogen-related receptor beta/NR3B2 controls epithelial cell fate and endolymph production by the stria vascularis.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE26668
Expression data from E13.5 Fz4-/-Fz8-/- and Fz4+/+Fz8-/- kidneys
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon

Description

Fz4 and Fz8 cooperate in regulating the branching morhpogenesis of the developing kidney during mouse embryonic development, hence determines the eventual kidney size.

Publication Title

Genetic mosaic analysis reveals a major role for frizzled 4 and frizzled 8 in controlling ureteric growth in the developing kidney.

Sample Metadata Fields

Specimen part

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accession-icon GSE23437
Gene regulation in the hyperoxia mouse retina
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon

Description

PURPOSE: Hyperoxia is toxic to photoreceptors, and this toxicity may be important in the progress of retinal dystrophies. This microarray study examines gene expression induced in the C57BL/6J mouse retina by hyperoxia over the 14-day period during which photoreceptors first resist, then succumb to, hyperoxia. METHODS: Young adult C57BL/6J mice were exposed to hyperoxia (75% oxygen) for up to 14 days. On day 0 (control), day 3, day 7, and day 14, retinal RNA was extracted and processed on Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Microarray data were analyzed using GCOS Version 1.4 and GeneSpring Version 7.3.1. RESULTS: The overall numbers of hyperoxia-regulated genes increased monotonically with exposure. Within that increase, however, a distinctive temporal pattern was apparent. At 3 days exposure, there was prominent upregulation of genes associated with neuroprotection. By day 14, these early-responsive genes were downregulated, and genes related to cell death were strongly expressed. At day 7, the regulation of these genes was mixed, indicating a possible transition period from stability at day 3 to degeneration at day 14. CONCLUSIONS: Microarray analysis of the response of the retina to prolonged hyperoxia demonstrated a temporal pattern involving early neuroprotection and later cell death, and provided insight into the mechanisms involved in the two phases of response. As hyperoxia is a consistent feature of the late stages of photoreceptor degenerations, understanding the mechanisms of oxygen toxicity may be important therapeutically.

Publication Title

Gene regulation induced in the C57BL/6J mouse retina by hyperoxia: a temporal microarray study.

Sample Metadata Fields

Specimen part

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accession-icon GSE16841
Transcriptional regulation by Norrin-Frizzled4 signaling
  • organism-icon Mus musculus
  • sample-icon 51 Downloadable Samples
  • Technology Badge Icon

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Norrin, frizzled-4, and Lrp5 signaling in endothelial cells controls a genetic program for retinal vascularization.

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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