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accession-icon GSE39442
Gene expression profiling in the developing neural tube
  • organism-icon Mus musculus
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

At an incidence of approximately 1/1000 births, neural tube defects (NTDs) comprise one of the most common and devastating congenital disorders. In an attempt to enhance and expand our understanding of neural tube closure, we undertook a high-throughput gene expression analysis of the neural tube as it was forming in the mouse embryo. Open and closed sections of the developing neural tube were micro-dissected from mouse embryos, and hybridized to Affymetrix mouse expression arrays. Clustering of genes differentially regulated in open and closed sections of the developing neural tube highlighted molecular processes previously recognized to be involved in neural tube closure and neurogenesis. Analysis of the genes in these categories identified potential candidates underlying neural tube closure. In addition, we identified approximately 25 novel genes, of unknown function, that were significantly up-regulated in the closed neural tube. Based on their expression patterns in the developing neural tube, five novel genes are proposed as interesting candidates for involvement in neurogenesis. The high-throughput expression analysis of the neural tube as it forms allows for better characterization of pathways involved in neural tube closure and neurogenesis, and hopefully will strengthen the foundation for further research along the pathways dictating neural tube development.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE38039
ZNF750 in late keratinocyte differentiation
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Disrupted skin barrier due to altered keratinocyte differentiation is common in pathologic conditions such as atopic dermatitis, ichthyosis and psoriasis. However, the molecular cascades governing keratinocyte terminal differentiation are still poorly understood. We have previously demonstrated that a dominant mutation in ZNF750 leads to a clinical phenotype that reminiscent of psoriasis and seborrheic dermatitis. We defined ZNF750 as a nuclear effector that is strongly activated in and essential for keratinocyte terminal differentiation. ZNF750 knockdown in HaCaT keratinocytes markedly reduced the expression of epidermal late differentiation markers, including gene subsets of epidermal differentiation complex and skin barrier formation such as FLG, LOR, SPINK5, ALOX12B and DSG1, known to be mutated in various human skin diseases. Furthermore, ZNF750 over-expression in undifferentiated cells induced terminal differentiation genes. Thus, ZNF750 is a regulator of keratinocyte terminal differentiation, and with its downstream targets can serve in future elucidation of therapeutics for common disease of skin barrier

Publication Title

ZNF750 is expressed in differentiated keratinocytes and regulates epidermal late differentiation genes.

Sample Metadata Fields

Specimen part

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accession-icon GSE73243
Expression data from U87 xenograft tissues
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

U87 xenograft tumors treated with scrambled siRNA (Tas_73, Tas_78) or siRNA against VDAC1 (Tas_57, Tas_61)

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE90852
Transcriptomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Arabidopsis Gene 1.0 ST Array (aragene10st)

Description

Even though accessions of one species are genetically very closely related to each other, they may show significantly different susceptibility or resistance towards abiotic and biotic stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance against the pathogen Pseudomonas syringae pv. tomato (Pst). To identify the molecular mechanisms contributing to this naturally occurring variety in resistance against Pst, we analysed changes in transcripts in Col-0 and C24 upon infection with Pst.

Publication Title

No associated publication

Sample Metadata Fields

Time

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accession-icon GSE14677
Expression data from rat kidney: pathophysiology of proteinuria
  • organism-icon Rattus norvegicus
  • sample-icon 51 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE14666
Expression data from female rat kidney: pathophysiology of proteinuria
  • organism-icon Rattus norvegicus
  • sample-icon 28 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This study was designed to investigate gene expression in kidneys of adult female Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria.

Publication Title

Geno-transcriptomic dissection of proteinuria in the uninephrectomized rat uncovers a molecular complexity with sexual dimorphism.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE14676
Expression data from male rat kidney: pathophysiology of proteinuria
  • organism-icon Rattus norvegicus
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

This study was designed to investigate gene expression in kidneys of adult Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE6787
Expression data from wildtype and Rb-/- fetal liver at e12.5
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

Rb null embryos exhibit defective fetal liver erythropoiesis. We used microarrays to compare Wt and Rb null fetal livers and to analyse gene expression differences which accompany and may underlie Rb null fetal liver degeneration, erythroid failure, and erythropoietic island dissolution.

Publication Title

Hypoxic stress underlies defects in erythroblast islands in the Rb-null mouse.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE99644
Transcriptome Profiling in KY1005-treated NHP HCT-recipients
  • organism-icon Macaca mulatta
  • sample-icon 100 Downloadable Samples
  • Technology Badge Icon Affymetrix Rhesus Macaque Genome Array (rhesus)

Description

Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD. In this study we specifically interrogated the transcriptional signatures of animals treated with KY1005 monotherapy and KY1005/Sirolimus combination therapy

Publication Title

Combined OX40L and mTOR blockade controls effector T cell activation while preserving T<sub>reg</sub> reconstitution after transplant.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE24427
Expression data of multiple sclerosis patients receiving subcutaneous Interferon-beta-1b therapy [U133 A and B]
  • organism-icon Homo sapiens
  • sample-icon 250 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

The purpose of this study was to characterize the transcriptional effects induced by subcutaneous IFN-beta-1b treatment (Betaferon, 250 g every other day) in patients with relapsing-remitting form of multiple sclerosis (MS).

Publication Title

Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-beta-1b treatment in relapsing remitting MS.

Sample Metadata Fields

Sex

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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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