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accession-icon GSE76027
Expression data of sciatic nerves from mice with Schwann-cell specific Sip1 deletion compared to control mice.
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Schwann cell maturation is tightly controlled by a set of transcriptional regulators. We have deleted the zinc-finger transcription factor Sip1 specifically from immature Schwann cells and observed a dramatic developmental delay.

Publication Title

Zeb2 is essential for Schwann cell differentiation, myelination and nerve repair.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE49703
Transcriptional profiles of CCR7lo effector memory human T cell subsets
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

The aim of this study was to identify differentially-expressed genes in CCR4hi/CXCR3- and CCR4lo CXCR3+ CCR6+ human Th17 cell subsets

Publication Title

Pro-inflammatory human Th17 cells selectively express P-glycoprotein and are refractory to glucocorticoids.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE49702
Expression profiling of MDR1+ and MDR1- human memory T cells from the blood and clinically-inflamed gut tissue
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

The aim of this study was to characterize the transcriptional signature of MDR1+ human memory T cells isolated from clinically inflamed gut tissue, and compare it to local MDR1- memory T cells

Publication Title

Pro-inflammatory human Th17 cells selectively express P-glycoprotein and are refractory to glucocorticoids.

Sample Metadata Fields

Specimen part

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accession-icon GSE19275
Muscle gene expression patterns in pigs with divergent phenotypes for fatness traits
  • organism-icon Sus scrofa
  • sample-icon 67 Downloadable Samples
  • Technology Badge Icon Affymetrix Porcine Genome Array (porcine)

Description

Background: Marketing products with added-value characteristics is a current trend in livestock production systems. Regarding meat, selection for intramuscular fat and muscular fatty acid composition is a way to improve the palatability and juiciness of meat while assuring a healthy fat content. This represents selecting animal with a different muscular metabolic profile with respect to the extended selection of lean animals. Results: The present study has analysed the muscular gene expression profiles of 68 commercial Duroc pigs belonging to two groups with extreme phenotypes for traits strongly related with lipid deposition and composition. This has allowed us to compare the physiological and metabolic implications of selecting for each of these extreme groups. Rather than upregulation of a single pathway, the main differences lied on the transcriptional levels of genes related with lipogenesis and lipolysis, revealing the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Most strikingly, several genes which enhanced fatty acid -oxidation and favoured insulin signalling and glucose uptake were upregulated in the fattest animals, indicating that the events leading to peripheral insulin resistance in humans with increased levels of intramuscular fat and obesity do not take place in these pigs. Moreover, neither was detected the well-characterised low-grade inflammatory state observed in overweighed humans. Conclusion: As a whole, our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to fully understand how lipid deposition affects muscle physiology in pigs.

Publication Title

Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE115887
Expression data from Drd2+ cells of mouse mPFC
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

The heterogeneity of cortical dopamine D2 receptor expressing cells is not well characterized

Publication Title

High Sensitivity Mapping of Cortical Dopamine D2 Receptor Expressing Neurons.

Sample Metadata Fields

Specimen part

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accession-icon GSE51980
CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Analysis of different iPSC clones in comparison to parental fibroblasts and Pluripotent ESC and iPSC lines

Publication Title

CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming.

Sample Metadata Fields

Cell line

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accession-icon GSE16879
Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatment
  • organism-icon Homo sapiens
  • sample-icon 132 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We used microarrays to identify mucosal gene signatures predictive of response to infliximab (IFX) in patients with inflammatory bowel disease (IBD) and to gain more insight into the pathogenesis of IBD.

Publication Title

Mucosal gene expression of antimicrobial peptides in inflammatory bowel disease before and after first infliximab treatment.

Sample Metadata Fields

Specimen part, Disease

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accession-icon GSE34901
Expression data from mouse lungs during E. coli pneumonia in the presence or absence of LIF neutralization
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Leukemia inhibitory factor (LIF) is amongst the IL-6 family cytokines expressed in the lungs during pneumonia. However, the function of endogenous LIF during pneumonia has never been explored. The purpose of this study was to determine the transcriptional response to pneumonia in the lungs and whether or how this response is influenced by LIF.

Publication Title

Leukemia inhibitory factor signaling is required for lung protection during pneumonia.

Sample Metadata Fields

Specimen part

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accession-icon GSE18975
Natural variation of auxin response
  • organism-icon Arabidopsis thaliana
  • sample-icon 83 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 M IAA.

Publication Title

Natural variation of transcriptional auxin response networks in Arabidopsis thaliana.

Sample Metadata Fields

Specimen part

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accession-icon GSE24207
mRNA analysis in different mouse tissues
  • organism-icon Mus musculus
  • sample-icon 73 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

The functioning of a specific tissue depends on the expression pattern of the different genes. We used microarrays to compare gene expression across different murine tissues, to get a better understanding in the expression pattern and functioning of the different tissues. With this analysis, we were not only able to identify genes that were specifically expressed in a spicific tissue but, as important, we also identified genes that were specifically repressed in a tissue, compared to al the other analysed tissues.

Publication Title

Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation.

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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