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accession-icon SRP063059
Transcriptome-wide Quantitative Analysis of XLPDR-derived human dermal fibroblasts with POLA1 deficiency
  • organism-icon Homo sapiens
  • sample-icon 26 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

The goal of this study is to analyzed transcriptome changes caused by POLA1 deficiency. Our data represents the first detailed analysis of molecular basis of XLPDR syndrome. We report than POLA1 deficiency leads to over-activation of IRF and NF-kB pathways with overexpression of typical markers of autoimmune syndromes. Overall design: Wild type and XLPDR-derived dermal fibroblasts are analyzed under non-stimulated (basal) conditions, after TNF treatment (2 and 12 h, 1000 U/mL), and poly(dA:dT) stimulation (16h, 1 mkg/mL). Obtained data were confirmed using the cellular model of XLPDR - normal dermal fibroblasts pretreated with control or anti-POLA1 siRNA and stimulated in analogous way.

Publication Title

NK cell defects in X-linked pigmentary reticulate disorder.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE68001
In vitro activation and reversion of human primary hepatic stellate cells
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U219 Array (hgu219)

Description

Liver fibrosis is characterized by the excessive formation and accumulation of matrix proteins as a result of wound healing in the liver. A main event during fibrogenesis is the activation of the liver resident quiescent hepatic stellate cell (qHSC). Recent studies suggest that reversion of the activated HSC (aHSC) phenotype into a quiescent-like phenotype could be a major cellular mechanism underlying fibrosis regression in the liver, thereby offering new therapeutic perspectives for the treatment of liver fibrosis. The goal of the present study is to identify experimental conditions that can revert the activated status of human HSCs and to map the molecular events associated with this phenotype reversion by gene expression profiling

Publication Title

In vitro reversion of activated primary human hepatic stellate cells.

Sample Metadata Fields

Sex, Age, Specimen part, Subject

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accession-icon GSE11511
Identification of histone codes and crosstalk in fission yeast
  • organism-icon Schizosaccharomyces pombe
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

Aims: To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. Using clustering analysis and gene ontology search tools, we identified promoter histone modification patterns that characterize several classes of gene function. For example, gene promoters of genes involved in cytokinesis have high H3K36me2 and low H3K4me2, whereas the converse pattern is found ar promoters of gene involved in positive regulation of the cell cycle. We detected acetylation of H4 preferentially at lysine 16 followed by lysine 12, 8 and 5. Our analysis shows that this H4 acetylation bias in the coding regions is dependent upon gene length and linked to gene expression. Our analysis also reveals a role for H3K36 methylation at gene promoters where it functions in a crosstalk between the histone methyltransferase Set2KMT3 and the histone deacetylase Clr6, which removes H3K27ac leading to repression of transcription. Conclusion: Histone modification patterns could be linked to gene expression in fission yeast.

Publication Title

Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE51882
Early Mouse Hepatic Stellate Cell Activation
  • organism-icon Mus musculus
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Early during culture of primary mouse HSCs gene expression changes.

Publication Title

Gene expression profiling of early hepatic stellate cell activation reveals a role for Igfbp3 in cell migration.

Sample Metadata Fields

Specimen part

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accession-icon GSE49995
Gene expression profiling and secretome analysis differentiate Adult-Derived Human Liver Stem/progenitor Cells and human hepatic stellate cells
  • organism-icon Homo sapiens
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U219 Array (hgu219)

Description

Adult-derived human liver stem/progenitor cells (ADHLSC) are obtained after primary culture of the liver parenchymal fraction. The cells are of fibroblastic morphology and exhibit a hepato-mesenchymal phenotype. Hepatic stellate cells (HSC) derived from the liver non-parenchymal fraction present a comparable morphology as ADHLSC. Because both ADHLSC and HSC are described as liver stem/progenitor cells, we strived to extensively compare both cell populations at different levels and to propose tools demonstrating their singularity.

Publication Title

Gene expression profiling and secretome analysis differentiate adult-derived human liver stem/progenitor cells and human hepatic stellate cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE153703
The Hippo pathway effector YAP controls mouse hepatic stellate cell activation
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

We identified the Hippo pathway and its effector YAP as a key pathway that controls stellate cell activation. YAP is a transcriptional co-activator and we found that it drives the earliest changes in gene expression during stellate cell activation.

Publication Title

The Hippo pathway effector YAP controls mouse hepatic stellate cell activation.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE36100
DKK2 Mediates Osteolysis, Invasiveness, and Metastatic Spread in Ewing Sarcoma
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Ewing sarcoma, an osteolytic malignancy that mainly affects children and young adults, is characterized

Publication Title

DKK2 mediates osteolysis, invasiveness, and metastatic spread in Ewing sarcoma.

Sample Metadata Fields

Cell line

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accession-icon GSE48010
Transcriptomic profiling of Ewing's sarcoma cell lines after knockdown of TRIP6
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This study aimed to explore the role of the Zyxin-related protein TRIP6 (thyroid receptor interacting protein 6) in Ewing's sarcoma (ES). By interrogation of published miccroarray data, we observed that of all seven Zyxin-proteins only TRIP6 is highly overexpressed in ES compared to normal tissues. RNA interference experiments and subsequent microarray and gene-set enrichment analyses indicated that TRIP6 expression is associated wth a pro-proliferative and pro-invasive transcriptional signature. Consistently, functional assays demonstrated that TRIP6 promotes migration, invasion, long-term proliferation and clonogencity of ES cells.

Publication Title

The Zyxin-related protein thyroid receptor interacting protein 6 (TRIP6) is overexpressed in Ewing's sarcoma and promotes migration, invasion and cell growth.

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE15606
Whole genome transcription profile of antigen receptor activated B cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

To search for rapid changes in gene expression following BCR activation, we performed DNA microarray analysis of activated splenic B cells with and without anti-IgM treatment for 3 hour. The expression of a remarkably large set of genes differed significantly.

Publication Title

Initiation of antigen receptor-dependent differentiation into plasma cells by calmodulin inhibition of E2A.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE34670
Gene expression in pediatric cALL
  • organism-icon Homo sapiens
  • sample-icon 37 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

Common ALL (cALL) is the most frequent entity of childhood ALL and carries an early pre-B cell phenotype. Expression patterns of 25 pediatric cALL samples were analyzed by use of high-density DNA microarrays HG-U133A.

Publication Title

MondoA is highly overexpressed in acute lymphoblastic leukemia cells and modulates their metabolism, differentiation and survival.

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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