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accession-icon GSE15894
Comparison of gene expression in whole blood of mice subjected to normobaric hypoxia in vivo.
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
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Description

To determine hypoxia mediated changes in whole blood, normal C57Bl/10 mice were gradually exposed to a chronic hypoxic environment, equivalent to an altitude of 6500m, for 2 weeks in vivo. Control, age-matched mice were maintained under normoxic, normobaric conditions by exposing them to ambient air in Philadelphia (c. 50 mts above sea level).

Publication Title

No associated publication

Sample Metadata Fields

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accession-icon GSE15902
Comparison of gene expression in whole blood of mice subjected to chemical hypoxia in vivo.
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon

Description

To understand hypoxia mediated changes in whole blood, normal C57Bl/10 mice were gradually exposed to a chronic chemical hypoxic environment, for 2 weeks. Control, age-machted mice were maintained under normoxic conditions.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE15901
Comparison of gene expression in whole blood of mice subjected to hypobaric hypoxia at Mt. Everest in vivo.
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
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Description

To determine hypoxia mediated changes in whole blood, normal swiss webster mice were gradually exposed to a chronic hypobaric hypoxic environment up to 8500m, for 2 weeks in vivo. Control, age-matched mice were maintained under normoxic conditions in Kathmandu (c. 1300 mts above sea level).

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE7038
RLSC and MMH-D3 cell lines
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
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Description

Increasing evidence provide support that the mammalian liver contains stem/progenitor cells, but their molecular phenotype, embryological derivation, cell biology as well as of their role in the liver cell turnover and regeneration remain to be further clarified.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE111392
Differentiation analysis of Mouse Posterior Neural tube
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
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Description

Posterior embryonic axis develops from neuromesodermal progenitors which differentiate into neural tube and paraxial mesoderm

Publication Title

Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesoderm <i>in vitro</i>.

Sample Metadata Fields

Treatment

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accession-icon GSE48600
Microarray expression analysis of wild type and Erg knockdown bone marrow hematopoietic stem and progenitor cells
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
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Description

Erg is an ETS family transcription factor frequently overexpressed in human leukemias and has been implicated as a key regulator of hematopoietic stem cells (HSCs). However how Erg controls normal hematopoiesis, particularly at the stem cell level, remains poorly understood. Using homologous recombination, we generated an Erg knockdown allele (Ergkd) in which Erg expression can be restored upon Cre-mediated excision of a Stopper cassette. In Ergkd/+ mice, ~40% reduction in Erg dosage perturbed both fetal liver and bone marrow hematopoiesis by reducing the numbers of Lin-Sca-1+c-Kit+ (LSK) hematopoietic stem and progenitor cells (HSPCs) and megakaryocytic progenitors.

Publication Title

Reduced Erg Dosage Impairs Survival of Hematopoietic Stem and Progenitor Cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE18500
Mast cells in response to some pathogens elicit a transcriptional program devoid of type I IFN response
  • organism-icon Mus musculus
  • sample-icon 35 Downloadable Samples
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Description

Although mast cells elicit proinflammatory and type I IFN responses upon VSV infection, in response to L.monocytogenes (L.m) or S. Typhimurium (S.t), such cells elicit a transcriptional program devoid of type I IFN response.

Publication Title

Mast cells elicit proinflammatory but not type I interferon responses upon activation of TLRs by bacteria.

Sample Metadata Fields

Specimen part

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accession-icon GSE18064
Comparison of MBT/Pas and BALB/cByJ MEFs response after infection with Rift Valley Fever virus
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon

Description

The Rift Valley Fever (RVF) is an arthropod-borne disease present in several countries of Africa and Middle East. It is caused by RVF virus which can infect both humans and animals. In humans, it leads to various manifestations including hepatitis, encephalitis and death, while in domestic animals it usually causes miscarriage in pregnant females and it is often fatal for the newborn. Not all people or animal infected by the virus present the same disease. Some patients exhibit unapparent or moderate febrile reactions, while others develop severe symptoms. This observation suggests that host genetic factors play a role in controlling the outcome of infection. In this work, we compare the response of two different inbred strains of mice, MBT/Pas and BALB/cByJ, to infection with RVF virus. These strains exhibit different profiles of susceptibility to RVF virus infection. Indeed, MBT/Pas mice rapidly develop high viraemia and die soon after infection, while BALB/cByJ mice have a lower viraemia and die later. Interestingly, mouse embryonic fibroblasts (MEFs) obtained from MBT/Pas foetuses allows higher viral production than BALB/cByJ MEFs.

Publication Title

A new mouse model reveals a critical role for host innate immunity in resistance to Rift Valley fever.

Sample Metadata Fields

Specimen part

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accession-icon GSE25244
Patterns of gene expression associated with temporal phases of S. aureus infection
  • organism-icon Mus musculus
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon

Description

To acquire more information regarding the local immune events during the different phases of S. aureus infection, gene profiling using microarray technology was used to identify host genes whose expression is substantively altered in the kidneys during the acute (T2) and persistent phase of infection (T28). Genes associated with the distinct transcript profiles were identified by comparing the relative abundance of transcripts at 2 days (acute) and 28 days (persistent) of infection to their abundance in the kidneys of uninfected control animals (CTL).

Publication Title

The dynamics of T cells during persistent Staphylococcus aureus infection: from antigen-reactivity to in vivo anergy.

Sample Metadata Fields

Specimen part

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accession-icon GSE27379
CD8+ T cell mediated lung inflammation
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon

Description

Role for naturally occurring CD4+CD25+Foxp3+ regulatory T cells (nTregs) in counterbalancing this process. Using a transgenic murine model for autoimmune-mediated lung disease, we demonstrated that, despite pulmonary inflammation, lung-specific CD8+ T cells can reside quiescently in close proximity to self-antigen. Whereas self-reactive CD8+ T cells in the inflamed lung and lung-draining lymph nodes down-regulated the expression of effector molecules, those located in the spleen appeared to be partly antigen-experienced and displayed a memory-like phenotype. Since ex vivo-reisolated self-reactive CD8+ T cells were very well capable to respond to the antigen in vitro, we investigated a possible contribution of nTregs to the immune control over autoaggressive CD8+ T cells in the lung.

Publication Title

CD4+CD25+Foxp3+ regulatory T cells are dispensable for controlling CD8+ T cell-mediated lung inflammation.

Sample Metadata Fields

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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