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accession-icon SRP141733
Human gut derived-organoids as model to study gluten response and effects of microbiota bioproducts in celiac disease
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Celiac disease (CeD) is an intestinal immune-mediated disorder caused by gluten ingestion in genetically predisposed subjects. CeD is characterized by villous atrophy, altered intestinal permeability, crypt hyperplasia and innate and adaptive immune response. This study aimed to develop and validate the use of intestinal organoids from celiac patients to study CeD. A repository of organoids from duodenum of non-celiac and celiac patients was generated and characterized accordingly to standard procedures. RNA-seq analysis was employed to study the global gene expression program of CeD (n=3) and non-CeD (n=3) organoids sets. While the three celiac derived organoids shared similar transcriptional signatures the NC samples set appeared more heterogeneous. We found 486 genes differentially expressed between the two groups. Of them, 299 genes were downregulated (FC<2; FDR<0.05) and 187 were upregulated in CeD (FC >2; FDR<0.05). We observed CeD organoids had significantly altered expression of genes associated with barrier function, innate immunity, and stem cell function. Overall design: mRNA profiles of 3 non-celiac healthy controls and 3 celiac organoids derived from duodenal biopsies.

Publication Title

Human gut derived-organoids provide model to study gluten response and effects of microbiota-derived molecules in celiac disease.

Sample Metadata Fields

Specimen part, Disease, Subject

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accession-icon GSE46293
Expression data of multiple sclerosis patients receiving Interferon-beta therapy
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), TaqMan(r) Array Human MicroRNA A Cards v2.0

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

MicroRNA expression changes during interferon-beta treatment in the peripheral blood of multiple sclerosis patients.

Sample Metadata Fields

Sex, Disease

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accession-icon GSE46280
Expression data of multiple sclerosis patients receiving Interferon-beta therapy [HG-U133_Plus_2]
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The purpose of this study was to investigate the expression dynamics of mRNAs and microRNAs in response to subcutaneous IFN-beta-1b treatment (Betaferon, 250 g every other day) in patients with clinically isolated syndrome (CIS) suggestive of multiple sclerosis (MS) or relapsing-remitting type of the disease (RRMS).

Publication Title

MicroRNA expression changes during interferon-beta treatment in the peripheral blood of multiple sclerosis patients.

Sample Metadata Fields

Sex, Disease

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accession-icon SRP137731
DDX6 decouples translational repression from RNA degradation of miRNA targets [ESC EpiLC 4sU]
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Translation and mRNA degradation are intimately connected, yet the mechanisms that regulate them are not fully understood. Here we examine the regulation of translation and mRNA stability in mouse embryonic stem cells (ESCs) and during differentiation. In contrast to previous reports, we found that transcriptional changes account for most of the molecular changes during ESC differentiation. Within ESCs translation level and mRNA stability are positively correlated. The RNA-binding protein DDX6 has been implicated in processes involving both translational repression and mRNA destabilization; in yeast DDX6 connects codon optimality and mRNA stability and in mammals DDX6 is involved in microRNA-mediated repression. We generated DDX6 KO ESCs and found that while there was minimal connection between codon usage and stability changes, the loss of DDX6 leads to the translational depression of microRNA targets. Surprisingly, the translational derepression of microRNA targets occurs without affecting mRNA stability. Furthermore, DDX6 KO ESCs share overlapping phenotypes and global molecular changes with ESCs that completely lack all microRNAs. Together our results demonstrate that the loss of DDX6 decouples the two forms of microRNA induced repression and emphasize that translational repression by microRNAs is underappreciated. Overall design: 4-thiouridine (4su) metabolic labeling was performed on mouse embryonic stem cells (ESCs) and Epiblast like cells (EpiLCs).

Publication Title

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells.

Sample Metadata Fields

Specimen part, Disease, Subject

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accession-icon GSE14323
RMA expression data for liver samples from subjects with HCV, HCV-HCC, or normal liver
  • organism-icon Homo sapiens
  • sample-icon 122 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

The role of chronic hepatitis C virus (HCV) in the pathogenesis of HCV-associated hepatocellular carcinoma (HCC) is not completely understood, particularly at the molecular level.

Publication Title

Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma.

Sample Metadata Fields

Specimen part

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accession-icon GSE32912
Expression profiling of attenuated mitochondrial function identifies retrograde signals in Drosophila
  • organism-icon Drosophila melanogaster
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Mitochondria are able to modulate cell state and fate during normal and pathophysiologic conditions through a nuclear mediated mechanism collectively termed as a retrograde response. Our previous studies in Drosophila have clearly established that progress through the cell cycle is precisely regulated by the intrinsic activity of the mitochondrion by specific signaling cascades mounted by the cell. As a means to further our understanding of how mitochondrial energy status affects nuclear control of basic cell decisions we have employed Affymetrix microarray-based transcriptional profiling of Drosophila S2 cells knocked down for the gene encoding subunit Va of the complex IV of the mitochondrial electron transport chain. The profiling data identifies up-regulation of glycolytic genes and metabolic studies confirm this increase in glycolysis. The transcriptional portrait which emerges implicates many signaling systems, including a p53 response, an insulin response, and up-regulation of conserved mitochondrial responses. This rich dataset provides many novel targets for further understanding the mechanism whereby the mitochondrion may direct cellular fate decisions. The data also provides a salient model of the shift of metabolism from a predominately oxidative state towards a predominately aerobic glycolytic state, and therefore provides a model of energy substrate management not unlike that found in cancer.

Publication Title

Expression profiling of attenuated mitochondrial function identifies retrograde signals in Drosophila.

Sample Metadata Fields

Cell line

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accession-icon GSE49331
Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia
  • organism-icon Mus musculus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia.

Sample Metadata Fields

Specimen part

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accession-icon GSE49329
Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia (mRNA)
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

The aim of this study was to determine the role that miRNAs have on influencing murine microgial phenotypes under M1(LPS) and M2a (IL-4) stimulating conditions.

Publication Title

Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia.

Sample Metadata Fields

Specimen part

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accession-icon GSE26440
Expression data for derivation of septic shock subgroups
  • organism-icon Homo sapiens
  • sample-icon 130 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Background: Septic shock is a heterogeneous syndrome within which probably exist several biological subclasses. Discovery and identification of septic shock subclasses could provide the foundation for the design of more specifically targeted therapies. Herein we tested the hypothesis that pediatric septic shock subclasses can be discovered through genome-wide expression profiling. Methods: Genome-wide expression profiling was conducted using whole blood-derived RNA from 98 children with septic shock, followed by a series of bioinformatic approaches targeted at subclass discovery and characterization. Results: Three putative subclasses (subclasses A, B, and C) were initially identified based on an empiric, discovery-oriented expression filter and unsupervised hierarchical clustering. Statistical comparison of the 3 putative subclasses (ANOVA, Bonferonni correction, p < 0.05) identified 6,934 differentially regulated genes. K means clustering of these 6,934 genes generated 10 coordinately regulated gene clusters corresponding to multiple signaling and metabolic pathways, all of which were differentially regulated across the 3 subclasses. Leave one out cross validation procedures indentified 100 genes having the strongest predictive values for subclass identification. Forty-four of these 100 genes corresponded to signaling pathways relevant to the adaptive immune system and glucocorticoid receptor signaling, the majority of which were repressed in subclass A patients. Subclass A patients were also characterized by repression of genes corresponding to zinc-related biology. Phenotypic analyses revealed that subclass A patients were younger, had a higher illness severity, and a higher mortality rate than patients in subclasses B and C. Conclusions: Genome-wide expression profiling can identify pediatric septic shock subclasses having clinically relevant phenotypes.

Publication Title

Identification of pediatric septic shock subclasses based on genome-wide expression profiling.

Sample Metadata Fields

Age, Specimen part, Disease, Disease stage

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accession-icon SRP095535
Multiple mechanisms of global microRNA suppression in vertebrate oocytes [RNA-seq]
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Mouse oocyte maturation, fertilization, and reprogramming occur in the absence of transcription and thus must be regulated post-transcriptionally. Surprisingly, a major form of post-transcriptional regulation, microRNA-based transcript destabilization and translational inhibition, is lost during this developmental window. Here we evaluate the conservation, timing, and mechanism behind the loss of microRNA activity in oocytes. In both mouse and frogs, microRNA function was active in growing oocytes, but then lost during oocyte maturation. RNA-sequencing of the maturing oocytes uncovered expression of an alternative isoform of Ago2 lacking domains critical for its function. Introduction of full-length Ago2 together with an exogenous microRNA destabilized microRNA luciferase reporters. However, endogenous targets were still largely unaffected. These findings suggest that while it is possible to re-activate some aspects of microRNA activity by introducing full length Ago2, there are additional mechanisms to protect endogenous transcripts from microRNA activity in oocytes. Overall design: Total RNA from mouse GV and MII oocytes, embryonic stem cells, epi cells

Publication Title

Expression of Alternative Ago2 Isoform Associated with Loss of microRNA-Driven Translational Repression in Mouse Oocytes.

Sample Metadata Fields

Specimen part, Subject

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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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