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accession-icon GSE103842
Respiratory Syncytial Virus Genotypes and Disease Severity in Young Children Hospitalized with Bronchiolitis
  • organism-icon Homo sapiens
  • sample-icon 74 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

Background: There is limited data on how different RSV genotypes and associated viral loads influence disease phenotypes. We characterized the genetic variability of RSV strains during five non-consecutive respiratory seasons, and evaluated the role of RSV subtypes, genotypes and viral loads on clinical disease severity.

Publication Title

Respiratory Syncytial Virus Genotypes, Host Immune Profiles, and Disease Severity in Young Children Hospitalized With Bronchiolitis.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE23396
Background analysis using yeast RNA on the mouse and human array
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

Sample Metadata Fields

Treatment

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accession-icon GSE22974
Background analysis using yeast RNA on the U133 plus 2.0 array
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We used yeast RNA to estimate background binding for each probe on the human U133 plus 2.0 array.

Publication Title

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

Sample Metadata Fields

Treatment

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accession-icon GSE22975
Background analysis using yeast RNA on the Mouse 430 2.0 array
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We hybridized yeast RNA to the mouse 430 2.0 array to estimate the background binding for each probe.

Publication Title

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

Sample Metadata Fields

Treatment

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accession-icon SRP153231
Transcriptional Profiling Identifies Novel Regulators of Macrophage Polarization [RNA-Seq]
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Identification of novel differentially expressed genes in human M1 and M2 macrophages using RNA-Seq Overall design: RNA-Seq was performed using RNA from M1 and M2-polarized macrophages from 4 biological replicates

Publication Title

Transcriptional profiling identifies novel regulators of macrophage polarization.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE94074
Expression data of Hematopoietic progenitor and stem cells after 18h of culture with or without extracellular vesicles secreted by AFT stromal cells
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Hematopoietic progenitor and stem cells from bone marrow have been sorted by FACS (LSK, Lineage -, Sca1 + and cKit +) and co-culture during 18h without cytokines with or without extracellular vesicles (EV) secreted by AFT stromal cells.

Publication Title

Extracellular vesicles of stromal origin target and support hematopoietic stem and progenitor cells.

Sample Metadata Fields

Specimen part

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accession-icon SRP198212
Differential gene expression in human RAF1 S257L/+ and isogenic corrected iPSC-derived cardiomyocytes
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIon Torrent S5

Description

Although several studies have uncovered abnormal signaling pathways in RASopathy disorders, little is known about the alterations of the cardiac transcriptome induced by Noonan syndrome (NS) mutations. Hence, to gain insights into the transcriptional alterations induced by the NS-associated RAF1S257L/+ mutation in human iPSC-derived cardiomyocytes, we performed quantitative transcriptome profiling by RNA-sequencing. Since we have found that inhibition of ERK5 and MEK1/2 pathways could normalized hypertrophy and myofibrillar disarray in mutant cardiomyocytes, we also aimed at identifying gene transcriptional profiles that were specifically affected by either MEK5-ERK5 or MEK1/2-ERK1/2 activation in RAF1S257L/+ iCMs. Overall design: mRNA profiles of human RAF1 S257L/+ and isogenic corrected iPSC-derived cardiomyocytes were generated by RNA-sequencing, in triplicate, using Ion S5.

Publication Title

Inducible Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Aberrant Extracellular Regulated Kinase 5 and Mitogen-Activated Protein Kinase Kinase 1/2 Signaling Concomitantly Promote Hypertrophic Cardiomyopathy in RAF1-Associated Noonan Syndrome.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE86181
Evidence of two distinct functionally specialized fibroblast lineages in breast stroma
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

Background: The terminal duct lobular unit (TDLU) is the most dynamic structure in the human breast and the putative site of origin of human breast cancer. Although stromal cells contribute to a specialized microenvironment in many organs, this component remains largely understudied in the human breast. We here demonstrate the impact on epithelium of two lineages of breast stromal fibroblasts, one of which accumulates in the TDLU while the other resides outside the TDLU in the interlobular stroma. Methods: The two lineages are prospectively isolated by FACS based on different expression levels of CD105 and CD26. The characteristics of the two fibroblast lineages are assessed by immunocytochemical staining and gene expression analysis. The differentiation capacity of the two fibroblast populations is determined by exposure to specific differentiating conditions followed by analysis of adipogenic and osteogenic differentiation. To test whether the two fibroblast lineages are functionally imprinted by their site of origin, single cell sorted CD271low/MUC1high normal breast luminal epithelial cells are plated on fibroblast feeders for the observation of morphological development. Epithelial structure formation and polarization is shown by immunofluorescence and digitalized quantification of immunoperoxidase stained cultures. Results: Lobular fibroblasts are CD105high/CD26low while interlobular fibroblasts are CD105low/CD26high. Once isolated the two lineages remain phenotypically stable and functionally distinct in culture. Lobular fibroblasts have properties in common with bone marrow derived mesenchymal stem cells and they specifically convey growth and branching morphogenesis of epithelial progenitors. Conclusions: Two distinct functionally specialized fibroblast lineages exist in the normal human breast, of which the lobular fibroblasts have properties in common with mesenchymal stem cells and support epithelial growth and morphogenesis. We propose that lobular fibroblasts constitute a specialized microenvironment for human breast luminal epithelial progenitors, i.e. the putative precursors of breast cancer.

Publication Title

Evidence of two distinct functionally specialized fibroblast lineages in breast stroma.

Sample Metadata Fields

Specimen part

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accession-icon GSE9914
Expression data from early symptomatic Sca1154Q/2Q and Sca7266Q/5Q knock-in cerebellum
  • organism-icon Mus musculus
  • sample-icon 22 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Comparative analysis of cerebellar gene expression changes occurring in Sca1154Q/2Q and Sca7266Q/5Q knock-in mice

Publication Title

The insulin-like growth factor pathway is altered in spinocerebellar ataxia type 1 and type 7.

Sample Metadata Fields

Sex, Age

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accession-icon GSE81244
Rspo1 role in mammary gland during pregnancy
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.1 ST Array (mogene11st)

Description

R-spondin1 (Rspo1) is a member of a secreted protein family which has pleiotropic functions in development and stem cell growth. Rspo1 knock-out mice are sex-reversed, but some remain sub-fertile, so, they are unable to nurse their pups. A lack of Rspo1 expression in mammary epithelial cells results in an absence of duct side-branching development and defective alveolar formation. In this study we propose to characterize the molecular functions involved to mammary gland phenotype due to Rspo1 knock out. By transcriptional profiling, we have identified gene misregulated in mammary gland of Rspo1 knock-out mice during pregnancy. A stronger expression of genes characterising mesenchymal tissue was observed in the absence of alterations to the structure of mammary epithelial tissue. Mammary epithelial cell characterization, by immunohistochemistry approach, revealed a persistence of virgin markers which sign a delay in their differentiation. Moreover serial transplantation experiments show that Rspo1 is associated with a regenerative potential of mammary epithelial cell control. Our data have also highlighted that in mammary gland during pregnancy the expression of Rspo1s partners, Lgr4 and RNF43, are negatively regulated and Tgf- signaling is modified in the absence of Rspo1. Taken together, our results show an abrupt halt in mammary development at mid-pregnancy due to loss of further differentiated function.

Publication Title

Phenotypic and Molecular Alterations in the Mammary Tissue of R-Spondin1 Knock-Out Mice during Pregnancy.

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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