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accession-icon GSE15516
Immunomodulatory function of bone marrow-derived mesenchymal stem cells in experimental autoimmune type 1 diabetes
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina mouse-6 v1.1 expression beadchips

Description

Human clinical trials in type 1 diabetes (T1D) patients are underway using mesenchymal stem cells (MSC) without prior validation in a mouse model for the disease. In response to this void, we characterized bone marrow-derived murine MSC for their ability to modulate immune responses in the context of T1D, as represented in non-obese diabetic (NOD) mice. In comparison to NOD-, BALB/c-MSC express higher levels of the negative costimulatory molecule PD-L1 and promote a shift toward Th2-like responses in treated NOD mice. In addition, transfer of MSC from resistant strains (i.e. NOR or BALB/c), but not from NOD mice, conferred disease protection when administered to prediabetic NOD mice. The number of BALB/c-MSC trafficking to the pancreatic lymph nodes of NOD mice was higher than in NOD mice provided autologous NOD-MSC. Administration of BALB/c-MSC resulted in reversal of hyperglycemia in 90% of NOD mice (p=0.002). Transfer of autologous NOD-MSC imparted no such therapeutic benefit, and in fact soft tissue and visceral tumors were uniquely observed in this setting (i.e. no tumors were present with BALB/c- or NOR-MSC transfer). These data provide important preclinical data supporting the basis for further development of allogeneic MSC-based therapies for T1D and potentially, other autoimmune disorders.

Publication Title

Immunomodulatory function of bone marrow-derived mesenchymal stem cells in experimental autoimmune type 1 diabetes.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-623
Transcription profiling of targeted overexpression of branchless (UAS-bn1) at different developmental stages, and of a bn1-P1 mutant in Drosophila
  • organism-icon Drosophila melanogaster
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

Transcriptome analysis of the targeted overexpression of branchless (UAS-bnl) using a tracheal driver (breathless-GAL4) in comparison to a wildtype reference at two different developmental stages (10-11h AEL and 17-19h AEL), and of a bnl-P1 mutant in comparison to a wildtype reference at 17-19h AEL.

Publication Title

Identification of FGF-dependent genes in the Drosophila tracheal system.

Sample Metadata Fields

Age, Time

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accession-icon GSE30239
Mis-expression of Tramtrack in Drosophila embryos
  • organism-icon Drosophila melanogaster
  • sample-icon 19 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

We profiled the transcriptome of Drosophila melanogaster embryos in ttk2D50 embryos or after over-expression using btl-GAL4; UAS-ttk, respectively. We further isolated cells that express btl-enh-RFPmoe (Cabernard and Affolter 2005) and FACS sorting, and profiled their transcriptomes in the same genetic backgrounds.

Publication Title

Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila.

Sample Metadata Fields

Specimen part

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accession-icon SRP067397
Transcriptomic profiling of alpha, beta, and delta cell populations provides new insights into the role of ghrelin in the pancreas
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Intra-islet crosstalk between islet cells is critical in orchestrating the body’s response to changes in blood glucose levels, but is incompletely understood. In this study, we used transgenic mouse lines that allowed the purification and transcriptomic characterisation of alpha, beta, and delta cells, yielding an RNA-sequencing database that can be searched for regulatory proteins which are differentially expressed between cell types. As an illustrative example, we examined the expression of g-protein coupled receptors, and found that the ghrelin receptor, Ghsr, was highly expressed in delta cells compared to alpha and beta cells. GHSR excitation elicited increases in cytosolic calcium levels in primary delta cells. In the perfused pancreas, the application of ghrelin stimulated somatostatin secretion, correlating with a decrease in insulin and glucagon release, which was sensitive to somatostatin receptor antagonism. These results show that ghrelin acts specifically on delta cells within pancreatic islets to affect blood glucose regulation. Overall design: Examination of transcriptomic profiles obtained from pancreatic alpha, beta and delta cells

Publication Title

Transcriptomic profiling of pancreatic alpha, beta and delta cell populations identifies delta cells as a principal target for ghrelin in mouse islets.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon SRP098982
Down-regulation of E protein activity augments an ILC2 differentiation program in the thymus
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Innate lymphoid cells (ILCs) are important regulators in various immune responses. Current paradigm states that all newly-made ILCs originate from common lymphoid progenitors (CLP) in the bone marrow. Id2, an inhibitor of E protein transcription factors, is indispensable for ILC differentiation. Unexpectedly, we found that ectopically expressing Id1 or deleting two E protein genes in the thymus drastically increased ILC2 counts in the thymus and other organs where ILC2 normally reside. Further evidence suggests a thymic origin of these mutant ILC2s. The mutant mice exhibit augmented spontaneous infiltration of eosinophils and heightened responses to papain in the lung and increased ability to expulse the helminth parasite, Nippostrongylus brasiliensis. These results prompt the question whether the thymus naturally has the capacity to produce ILC2s and E proteins restrain such a potential. The abundance of ILC2s in Id1 transgenic mice also offers a unique opportunity for testing the biological functions of ILC2s. Overall design: For RNA-seq analyses, ILC2s (Lin-Thy1+ST2+) were sorted from thymocytes and mesenteric lymph node cells and processed for RNA-seq. In addition, MLN cells were also cultured in the presence of IL-, IL-25 and IL33. Duplicate samples were analyzed.

Publication Title

Downregulation of E Protein Activity Augments an ILC2 Differentiation Program in the Thymus.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE58857
A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression.

Publication Title

Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.

Sample Metadata Fields

Specimen part

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accession-icon GSE58855
A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression.

Publication Title

Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE71031
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st), Illumina Genome Analyzer IIx

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3.

Sample Metadata Fields

Cell line, Time

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accession-icon GSE70805
Gene expression profiling in MCF7 cell lines under hypoxia and reoxygenation
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx, Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Purpose: Study hypoxia and reoxygenation induced changes in genome-wide gene expression

Publication Title

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.

Sample Metadata Fields

Cell line, Time

View Samples
accession-icon GSE55232
Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart
  • organism-icon Homo sapiens
  • sample-icon 129 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples

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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